Starting phenix.real_space_refine on Sat Jun 28 15:27:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l43_62804/06_2025/9l43_62804.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l43_62804/06_2025/9l43_62804.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9l43_62804/06_2025/9l43_62804.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l43_62804/06_2025/9l43_62804.map" model { file = "/net/cci-nas-00/data/ceres_data/9l43_62804/06_2025/9l43_62804.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l43_62804/06_2025/9l43_62804.cif" } resolution = 3.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.069 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 S 121 5.16 5 C 11058 2.51 5 N 2915 2.21 5 O 3170 1.98 5 H 15995 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 71 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 33261 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 11843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 827, 11843 Classifications: {'peptide': 827} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 800} Chain breaks: 6 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 550 Unresolved non-hydrogen angles: 693 Unresolved non-hydrogen dihedrals: 470 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 11, 'TYR:plan': 4, 'ASN:plan1': 4, 'TRP:plan': 2, 'HIS:plan': 5, 'PHE:plan': 12, 'GLU:plan': 9, 'ASP:plan': 14} Unresolved non-hydrogen planarities: 300 Chain: "B" Number of atoms: 11860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 853, 11860 Classifications: {'peptide': 853} Link IDs: {'PTRANS': 28, 'TRANS': 824} Chain breaks: 6 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 663 Unresolved non-hydrogen angles: 833 Unresolved non-hydrogen dihedrals: 540 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'GLN:plan1': 14, 'ASP:plan': 12, 'TYR:plan': 4, 'ASN:plan1': 7, 'TRP:plan': 1, 'HIS:plan': 5, 'PHE:plan': 7, 'GLU:plan': 10, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 327 Chain: "D" Number of atoms: 4754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 4754 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 18, 'TRANS': 347} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 322 Unresolved non-hydrogen angles: 407 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 4, 'ASN:plan1': 2, 'HIS:plan': 5, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 171 Chain: "C" Number of atoms: 4802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 4802 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 18, 'TRANS': 350} Chain breaks: 6 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 308 Unresolved non-hydrogen angles: 393 Unresolved non-hydrogen dihedrals: 238 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 3, 'GLU:plan': 4, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 146 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 26553 SG CYS D 624 94.572 55.167 63.585 1.00 96.81 S ATOM 26620 SG CYS D 630 93.161 54.159 65.004 1.00 95.49 S ATOM 27198 SG CYS D 680 95.128 53.016 63.718 1.00112.06 S ATOM 27224 SG CYS D 682 93.318 51.943 64.526 1.00107.42 S ATOM 31350 SG CYS C 624 25.701 121.150 61.595 1.00 50.00 S ATOM 31374 SG CYS C 630 27.507 121.772 62.967 1.00 90.83 S ATOM 31968 SG CYS C 680 25.601 123.311 63.171 1.00105.62 S ATOM 31985 SG CYS C 682 27.792 123.933 63.017 1.00 94.89 S Time building chain proxies: 15.60, per 1000 atoms: 0.47 Number of scatterers: 33261 At special positions: 0 Unit cell: (120.91, 178.69, 100.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 121 16.00 O 3170 8.00 N 2915 7.00 C 11058 6.00 H 15995 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 128 " distance=2.05 Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 507 " distance=2.03 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 507 " distance=2.03 Simple disulfide: pdb=" SG CYS D 330 " - pdb=" SG CYS C 330 " distance=2.07 Simple disulfide: pdb=" SG CYS C 394 " - pdb=" SG CYS C 411 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.91 Conformation dependent library (CDL) restraints added in 2.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 801 " pdb="ZN ZN C 801 " - pdb=" SG CYS C 680 " pdb="ZN ZN C 801 " - pdb=" SG CYS C 630 " pdb="ZN ZN C 801 " - pdb=" SG CYS C 624 " pdb="ZN ZN C 801 " - pdb=" SG CYS C 682 " pdb=" ZN D 801 " pdb="ZN ZN D 801 " - pdb=" SG CYS D 630 " pdb="ZN ZN D 801 " - pdb=" SG CYS D 680 " pdb="ZN ZN D 801 " - pdb=" SG CYS D 624 " pdb="ZN ZN D 801 " - pdb=" SG CYS D 682 " Number of angles added : 12 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4646 Finding SS restraints... Secondary structure from input PDB file: 131 helices and 2 sheets defined 78.8% alpha, 0.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.50 Creating SS restraints... Processing helix chain 'A' and resid 10 through 19 Processing helix chain 'A' and resid 27 through 46 Proline residue: A 33 - end of helix Processing helix chain 'A' and resid 48 through 55 removed outlier: 3.732A pdb=" N GLU A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU A 55 " --> pdb=" O VAL A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.640A pdb=" N MET A 67 " --> pdb=" O PRO A 63 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LYS A 77 " --> pdb=" O GLN A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 112 Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 116 through 137 removed outlier: 4.688A pdb=" N LYS A 121 " --> pdb=" O HIS A 117 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N LYS A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 165 removed outlier: 3.971A pdb=" N PHE A 142 " --> pdb=" O SER A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 185 removed outlier: 4.040A pdb=" N HIS A 185 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 221 removed outlier: 6.191A pdb=" N ALA A 218 " --> pdb=" O THR A 214 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ILE A 219 " --> pdb=" O ARG A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 239 Processing helix chain 'A' and resid 241 through 260 Processing helix chain 'A' and resid 262 through 280 removed outlier: 3.669A pdb=" N ALA A 266 " --> pdb=" O PRO A 262 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N SER A 267 " --> pdb=" O ALA A 263 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N THR A 268 " --> pdb=" O GLN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 283 No H-bonds generated for 'chain 'A' and resid 281 through 283' Processing helix chain 'A' and resid 284 through 303 removed outlier: 4.480A pdb=" N GLU A 293 " --> pdb=" O LYS A 289 " (cutoff:3.500A) Proline residue: A 294 - end of helix Processing helix chain 'A' and resid 314 through 331 removed outlier: 3.755A pdb=" N LEU A 318 " --> pdb=" O GLU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 339 through 355 Processing helix chain 'A' and resid 364 through 381 removed outlier: 3.958A pdb=" N ARG A 368 " --> pdb=" O ALA A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 391 No H-bonds generated for 'chain 'A' and resid 389 through 391' Processing helix chain 'A' and resid 392 through 412 removed outlier: 4.187A pdb=" N LEU A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 481 Processing helix chain 'A' and resid 488 through 506 Processing helix chain 'A' and resid 507 through 509 No H-bonds generated for 'chain 'A' and resid 507 through 509' Processing helix chain 'A' and resid 536 through 554 removed outlier: 3.646A pdb=" N TYR A 540 " --> pdb=" O SER A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 580 removed outlier: 4.165A pdb=" N GLU A 560 " --> pdb=" O LYS A 556 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ALA A 561 " --> pdb=" O LEU A 557 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR A 562 " --> pdb=" O ASP A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 596 removed outlier: 3.820A pdb=" N LEU A 587 " --> pdb=" O GLU A 583 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASP A 589 " --> pdb=" O HIS A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 611 removed outlier: 4.056A pdb=" N LYS A 609 " --> pdb=" O ASP A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 625 Processing helix chain 'A' and resid 626 through 628 No H-bonds generated for 'chain 'A' and resid 626 through 628' Processing helix chain 'A' and resid 629 through 643 removed outlier: 3.517A pdb=" N PHE A 643 " --> pdb=" O LEU A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 661 Processing helix chain 'A' and resid 664 through 683 removed outlier: 5.137A pdb=" N ILE A 677 " --> pdb=" O SER A 673 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN A 682 " --> pdb=" O LEU A 678 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ASN A 683 " --> pdb=" O LEU A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 695 Processing helix chain 'A' and resid 701 through 718 removed outlier: 3.843A pdb=" N GLY A 712 " --> pdb=" O ALA A 708 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLN A 713 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N CYS A 716 " --> pdb=" O GLY A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 784 Processing helix chain 'A' and resid 785 through 792 removed outlier: 3.861A pdb=" N HIS A 792 " --> pdb=" O HIS A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 815 removed outlier: 4.219A pdb=" N LEU A 812 " --> pdb=" O THR A 808 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N MET A 813 " --> pdb=" O LEU A 809 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLU A 814 " --> pdb=" O LEU A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 823 removed outlier: 3.650A pdb=" N VAL A 822 " --> pdb=" O LYS A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 835 Processing helix chain 'A' and resid 840 through 861 Processing helix chain 'A' and resid 862 through 880 Processing helix chain 'A' and resid 883 through 897 Processing helix chain 'A' and resid 900 through 918 removed outlier: 3.761A pdb=" N SER A 904 " --> pdb=" O SER A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 949 removed outlier: 5.810A pdb=" N LYS A 931 " --> pdb=" O SER A 927 " (cutoff:3.500A) Proline residue: A 932 - end of helix Processing helix chain 'B' and resid 11 through 17 Processing helix chain 'B' and resid 25 through 45 removed outlier: 3.795A pdb=" N LYS B 32 " --> pdb=" O THR B 28 " (cutoff:3.500A) Proline residue: B 33 - end of helix removed outlier: 3.596A pdb=" N ARG B 43 " --> pdb=" O GLN B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 51 removed outlier: 3.789A pdb=" N VAL B 50 " --> pdb=" O ASP B 47 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N VAL B 51 " --> pdb=" O VAL B 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 47 through 51' Processing helix chain 'B' and resid 65 through 79 removed outlier: 3.562A pdb=" N LEU B 69 " --> pdb=" O SER B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 83 Processing helix chain 'B' and resid 94 through 109 Processing helix chain 'B' and resid 116 through 138 removed outlier: 3.906A pdb=" N LYS B 121 " --> pdb=" O HIS B 117 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N LYS B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N SER B 129 " --> pdb=" O GLU B 125 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU B 130 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 131 " --> pdb=" O ILE B 127 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N PHE B 132 " --> pdb=" O CYS B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 165 Processing helix chain 'B' and resid 198 through 221 removed outlier: 6.242A pdb=" N ALA B 218 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ILE B 219 " --> pdb=" O ARG B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 239 removed outlier: 3.925A pdb=" N LEU B 227 " --> pdb=" O ARG B 223 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU B 228 " --> pdb=" O ARG B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 260 Processing helix chain 'B' and resid 262 through 281 removed outlier: 3.734A pdb=" N ALA B 266 " --> pdb=" O PRO B 262 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N SER B 267 " --> pdb=" O ALA B 263 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N THR B 268 " --> pdb=" O GLN B 264 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VAL B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 303 removed outlier: 5.230A pdb=" N GLU B 293 " --> pdb=" O LYS B 289 " (cutoff:3.500A) Proline residue: B 294 - end of helix Processing helix chain 'B' and resid 314 through 331 removed outlier: 3.632A pdb=" N LEU B 318 " --> pdb=" O GLU B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 337 Processing helix chain 'B' and resid 339 through 356 Processing helix chain 'B' and resid 364 through 383 removed outlier: 3.854A pdb=" N ARG B 368 " --> pdb=" O ALA B 364 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU B 383 " --> pdb=" O LEU B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 386 No H-bonds generated for 'chain 'B' and resid 384 through 386' Processing helix chain 'B' and resid 389 through 391 No H-bonds generated for 'chain 'B' and resid 389 through 391' Processing helix chain 'B' and resid 392 through 411 Processing helix chain 'B' and resid 412 through 414 No H-bonds generated for 'chain 'B' and resid 412 through 414' Processing helix chain 'B' and resid 460 through 480 removed outlier: 3.793A pdb=" N SER B 480 " --> pdb=" O SER B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 507 Processing helix chain 'B' and resid 536 through 553 removed outlier: 4.195A pdb=" N ARG B 548 " --> pdb=" O LEU B 544 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER B 549 " --> pdb=" O LYS B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 580 Processing helix chain 'B' and resid 583 through 596 removed outlier: 3.879A pdb=" N GLY B 592 " --> pdb=" O GLU B 588 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N MET B 593 " --> pdb=" O ASP B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 601 removed outlier: 4.509A pdb=" N TYR B 600 " --> pdb=" O LEU B 596 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N SER B 601 " --> pdb=" O PRO B 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 596 through 601' Processing helix chain 'B' and resid 605 through 611 removed outlier: 3.514A pdb=" N LYS B 609 " --> pdb=" O ASP B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 625 removed outlier: 3.925A pdb=" N ASN B 616 " --> pdb=" O THR B 612 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N THR B 619 " --> pdb=" O ALA B 615 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N LEU B 620 " --> pdb=" O ASN B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 628 No H-bonds generated for 'chain 'B' and resid 626 through 628' Processing helix chain 'B' and resid 629 through 643 Processing helix chain 'B' and resid 648 through 661 removed outlier: 3.552A pdb=" N GLN B 661 " --> pdb=" O ASN B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 683 removed outlier: 5.589A pdb=" N ILE B 677 " --> pdb=" O SER B 673 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLN B 680 " --> pdb=" O PHE B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 698 Processing helix chain 'B' and resid 700 through 718 removed outlier: 3.916A pdb=" N LYS B 704 " --> pdb=" O SER B 700 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLN B 713 " --> pdb=" O SER B 709 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N CYS B 716 " --> pdb=" O GLY B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 768 Processing helix chain 'B' and resid 775 through 793 removed outlier: 3.667A pdb=" N LYS B 779 " --> pdb=" O PRO B 775 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N HIS B 787 " --> pdb=" O ILE B 783 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N HIS B 788 " --> pdb=" O ASP B 784 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LYS B 791 " --> pdb=" O HIS B 787 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N HIS B 792 " --> pdb=" O HIS B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 811 Processing helix chain 'B' and resid 818 through 835 removed outlier: 4.343A pdb=" N LYS B 829 " --> pdb=" O SER B 825 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N HIS B 830 " --> pdb=" O GLY B 826 " (cutoff:3.500A) Processing helix chain 'B' and resid 839 through 861 Processing helix chain 'B' and resid 862 through 880 Processing helix chain 'B' and resid 883 through 896 removed outlier: 3.525A pdb=" N PHE B 887 " --> pdb=" O ASP B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 903 through 911 removed outlier: 4.767A pdb=" N THR B 909 " --> pdb=" O GLY B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 922 through 942 removed outlier: 5.234A pdb=" N LYS B 931 " --> pdb=" O SER B 927 " (cutoff:3.500A) Proline residue: B 932 - end of helix removed outlier: 3.840A pdb=" N GLU B 939 " --> pdb=" O GLN B 935 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N SER B 940 " --> pdb=" O PHE B 936 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 318 Processing helix chain 'D' and resid 329 through 334 Processing helix chain 'D' and resid 374 through 392 Processing helix chain 'D' and resid 413 through 418 Processing helix chain 'D' and resid 419 through 434 Processing helix chain 'D' and resid 468 through 489 removed outlier: 3.979A pdb=" N GLY D 473 " --> pdb=" O CYS D 469 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE D 474 " --> pdb=" O ILE D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 490 through 498 Processing helix chain 'D' and resid 536 through 552 removed outlier: 3.820A pdb=" N LYS D 540 " --> pdb=" O HIS D 536 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU D 545 " --> pdb=" O MET D 541 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA D 547 " --> pdb=" O LEU D 543 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N PHE D 548 " --> pdb=" O HIS D 544 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA D 552 " --> pdb=" O PHE D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 554 through 557 Processing helix chain 'D' and resid 558 through 575 removed outlier: 4.197A pdb=" N THR D 562 " --> pdb=" O ALA D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 588 removed outlier: 3.783A pdb=" N CYS D 585 " --> pdb=" O ARG D 582 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 595 Processing helix chain 'D' and resid 599 through 615 Processing helix chain 'D' and resid 616 through 623 removed outlier: 3.695A pdb=" N ALA D 620 " --> pdb=" O ASP D 617 " (cutoff:3.500A) Proline residue: D 621 - end of helix Processing helix chain 'D' and resid 633 through 641 Processing helix chain 'D' and resid 648 through 670 removed outlier: 4.181A pdb=" N SER D 670 " --> pdb=" O LEU D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 682 through 705 removed outlier: 4.322A pdb=" N VAL D 687 " --> pdb=" O ASN D 683 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG D 688 " --> pdb=" O VAL D 684 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N THR D 700 " --> pdb=" O ARG D 696 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG D 702 " --> pdb=" O TRP D 698 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ARG D 703 " --> pdb=" O LEU D 699 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA D 704 " --> pdb=" O THR D 700 " (cutoff:3.500A) Processing helix chain 'D' and resid 710 through 733 Processing helix chain 'D' and resid 736 through 742 Processing helix chain 'D' and resid 744 through 762 Proline residue: D 753 - end of helix Processing helix chain 'D' and resid 766 through 776 Processing helix chain 'C' and resid 310 through 317 removed outlier: 4.434A pdb=" N ASN C 314 " --> pdb=" O SER C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 334 Processing helix chain 'C' and resid 371 through 390 Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 419 through 440 removed outlier: 3.755A pdb=" N VAL C 423 " --> pdb=" O PHE C 419 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N HIS C 430 " --> pdb=" O PHE C 426 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ALA C 433 " --> pdb=" O LEU C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 489 Processing helix chain 'C' and resid 490 through 498 Processing helix chain 'C' and resid 536 through 551 removed outlier: 3.536A pdb=" N ALA C 547 " --> pdb=" O LEU C 543 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE C 548 " --> pdb=" O HIS C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 574 Processing helix chain 'C' and resid 579 through 588 removed outlier: 4.922A pdb=" N CYS C 585 " --> pdb=" O ARG C 582 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN C 588 " --> pdb=" O CYS C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 594 removed outlier: 3.553A pdb=" N CYS C 593 " --> pdb=" O VAL C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 614 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 631 through 641 Processing helix chain 'C' and resid 648 through 668 Processing helix chain 'C' and resid 680 through 702 removed outlier: 4.589A pdb=" N VAL C 687 " --> pdb=" O ASN C 683 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ARG C 688 " --> pdb=" O VAL C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 703 through 705 No H-bonds generated for 'chain 'C' and resid 703 through 705' Processing helix chain 'C' and resid 710 through 734 Processing helix chain 'C' and resid 736 through 742 Processing helix chain 'C' and resid 744 through 762 Proline residue: C 753 - end of helix Processing helix chain 'C' and resid 766 through 777 removed outlier: 3.678A pdb=" N CYS C 777 " --> pdb=" O LEU C 773 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 454 through 455 removed outlier: 8.026A pdb=" N VAL A 454 " --> pdb=" O THR A 533 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 452 through 453 removed outlier: 6.666A pdb=" N LYS B 452 " --> pdb=" O VAL B 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 1252 hydrogen bonds defined for protein. 3687 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.81 Time building geometry restraints manager: 10.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.05: 15941 1.05 - 1.26: 2957 1.26 - 1.47: 6601 1.47 - 1.68: 7863 1.68 - 1.89: 173 Bond restraints: 33535 Sorted by residual: bond pdb=" CA LEU C 623 " pdb=" C LEU C 623 " ideal model delta sigma weight residual 1.523 1.689 -0.166 1.34e-02 5.57e+03 1.53e+02 bond pdb=" C CYS C 624 " pdb=" N SER C 625 " ideal model delta sigma weight residual 1.333 1.248 0.085 1.45e-02 4.76e+03 3.42e+01 bond pdb=" CA CYS C 624 " pdb=" C CYS C 624 " ideal model delta sigma weight residual 1.524 1.453 0.071 1.26e-02 6.30e+03 3.21e+01 bond pdb=" N LEU C 631 " pdb=" CA LEU C 631 " ideal model delta sigma weight residual 1.459 1.523 -0.064 1.21e-02 6.83e+03 2.76e+01 bond pdb=" ND1 HIS C 488 " pdb=" CE1 HIS C 488 " ideal model delta sigma weight residual 1.321 1.373 -0.052 1.00e-02 1.00e+04 2.75e+01 ... (remaining 33530 not shown) Histogram of bond angle deviations from ideal: 0.00 - 20.87: 60537 20.87 - 41.74: 10 41.74 - 62.61: 0 62.61 - 83.48: 1 83.48 - 104.35: 1 Bond angle restraints: 60549 Sorted by residual: angle pdb="HD22 LEU D 312 " pdb=" CD2 LEU D 312 " pdb="HD23 LEU D 312 " ideal model delta sigma weight residual 110.00 5.65 104.35 3.00e+00 1.11e-01 1.21e+03 angle pdb="HD22 LEU A 642 " pdb=" CD2 LEU A 642 " pdb="HD23 LEU A 642 " ideal model delta sigma weight residual 110.00 27.27 82.73 3.00e+00 1.11e-01 7.60e+02 angle pdb=" O GLN C 622 " pdb=" C GLN C 622 " pdb=" N LEU C 623 " ideal model delta sigma weight residual 122.59 90.11 32.48 1.33e+00 5.65e-01 5.96e+02 angle pdb=" N VAL A 822 " pdb=" CA VAL A 822 " pdb=" CB VAL A 822 " ideal model delta sigma weight residual 112.36 83.74 28.62 1.30e+00 5.92e-01 4.85e+02 angle pdb=" C CYS C 624 " pdb=" CA CYS C 624 " pdb=" CB CYS C 624 " ideal model delta sigma weight residual 110.77 86.61 24.16 1.67e+00 3.59e-01 2.09e+02 ... (remaining 60544 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 14248 17.62 - 35.25: 1252 35.25 - 52.87: 402 52.87 - 70.49: 122 70.49 - 88.12: 16 Dihedral angle restraints: 16040 sinusoidal: 8062 harmonic: 7978 Sorted by residual: dihedral pdb=" C HIS C 626 " pdb=" N HIS C 626 " pdb=" CA HIS C 626 " pdb=" CB HIS C 626 " ideal model delta harmonic sigma weight residual -122.60 -151.42 28.82 0 2.50e+00 1.60e-01 1.33e+02 dihedral pdb=" N VAL A 822 " pdb=" C VAL A 822 " pdb=" CA VAL A 822 " pdb=" CB VAL A 822 " ideal model delta harmonic sigma weight residual 123.40 96.38 27.02 0 2.50e+00 1.60e-01 1.17e+02 dihedral pdb=" CA GLN C 622 " pdb=" C GLN C 622 " pdb=" N LEU C 623 " pdb=" CA LEU C 623 " ideal model delta harmonic sigma weight residual 180.00 126.75 53.25 0 5.00e+00 4.00e-02 1.13e+02 ... (remaining 16037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.215: 2956 0.215 - 0.429: 5 0.429 - 0.644: 2 0.644 - 0.858: 0 0.858 - 1.073: 1 Chirality restraints: 2964 Sorted by residual: chirality pdb=" CA HIS C 626 " pdb=" N HIS C 626 " pdb=" C HIS C 626 " pdb=" CB HIS C 626 " both_signs ideal model delta sigma weight residual False 2.51 1.44 1.07 2.00e-01 2.50e+01 2.88e+01 chirality pdb=" CA PHE D 383 " pdb=" N PHE D 383 " pdb=" C PHE D 383 " pdb=" CB PHE D 383 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.04e+00 chirality pdb=" CA ARG A 821 " pdb=" N ARG A 821 " pdb=" C ARG A 821 " pdb=" CB ARG A 821 " both_signs ideal model delta sigma weight residual False 2.51 2.94 -0.43 2.00e-01 2.50e+01 4.69e+00 ... (remaining 2961 not shown) Planarity restraints: 5327 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 683 " -0.254 2.00e-02 2.50e+03 3.30e-01 1.64e+03 pdb=" CG ASN C 683 " 0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN C 683 " 0.248 2.00e-02 2.50e+03 pdb=" ND2 ASN C 683 " 0.004 2.00e-02 2.50e+03 pdb="HD21 ASN C 683 " -0.521 2.00e-02 2.50e+03 pdb="HD22 ASN C 683 " 0.507 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 35 " 0.229 2.00e-02 2.50e+03 2.80e-01 1.18e+03 pdb=" CD GLN A 35 " -0.022 2.00e-02 2.50e+03 pdb=" OE1 GLN A 35 " -0.212 2.00e-02 2.50e+03 pdb=" NE2 GLN A 35 " -0.006 2.00e-02 2.50e+03 pdb="HE21 GLN A 35 " -0.427 2.00e-02 2.50e+03 pdb="HE22 GLN A 35 " 0.438 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 622 " -0.112 2.00e-02 2.50e+03 1.79e-01 3.22e+02 pdb=" C GLN C 622 " 0.310 2.00e-02 2.50e+03 pdb=" O GLN C 622 " -0.105 2.00e-02 2.50e+03 pdb=" N LEU C 623 " -0.093 2.00e-02 2.50e+03 ... (remaining 5324 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.07: 658 2.07 - 2.70: 53539 2.70 - 3.34: 98307 3.34 - 3.97: 112294 3.97 - 4.60: 177040 Nonbonded interactions: 441838 Sorted by model distance: nonbonded pdb=" HZ3 LYS A 818 " pdb=" OE2 GLU A 864 " model vdw 1.439 2.450 nonbonded pdb=" O THR B 504 " pdb=" HG SER B 508 " model vdw 1.457 2.450 nonbonded pdb=" O TRP A 598 " pdb=" HG SER A 601 " model vdw 1.486 2.450 nonbonded pdb=" O VAL A 688 " pdb=" HZ2 LYS A 690 " model vdw 1.489 2.450 nonbonded pdb=" O LEU B 740 " pdb=" H ARG B 743 " model vdw 1.496 2.450 ... (remaining 441833 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 10 and (name N or name CA or name C or name O or name CB \ or name OG or name HA or name HB2 or name HB3 or name HG )) or resid 11 through \ 12 or (resid 13 and (name N or name CA or name C or name O or name CB or name HA \ )) or resid 14 through 15 or (resid 16 through 17 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 18 through 28 or (resi \ d 29 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 30 through 38 or (resid 39 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 40 through 42 or (resid 43 and (na \ me N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 44 through 55 or (resid 64 and (name N or name CA or name C or name O or name CB \ or name HA )) or resid 65 through 66 or (resid 67 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 68 or (resid 69 throug \ h 70 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 71 or (resid 72 and (name N or name CA or name C or name O or name C \ B or name H or name HA )) or resid 73 through 76 or (resid 77 and (name N or nam \ e CA or name C or name O or name CB or name H or name HA )) or resid 78 through \ 85 or (resid 93 and (name N or name CA or name C or name O or name CB or name HA \ )) or resid 94 through 97 or (resid 98 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 99 through 116 or (resid 117 thro \ ugh 118 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 119 through 123 or (resid 124 through 129 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 130 or (resid 13 \ 1 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 132 through 135 or (resid 136 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 137 through 144 or (resid 145 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or res \ id 146 through 147 or (resid 148 and (name N or name CA or name C or name O or n \ ame CB or name H or name HA )) or resid 149 through 183 or (resid 192 and (name \ N or name CA or name C or name O or name CB or name HA or name HB1 or name HB2 o \ r name HB3)) or resid 193 through 195 or (resid 196 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 197 or (resid 198 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or re \ sid 199 or (resid 200 and (name N or name CA or name C or name O or name CB or n \ ame H or name HA )) or resid 201 through 216 or (resid 217 and (name N or name C \ A or name C or name O or name CB or name H or name HA )) or resid 218 through 22 \ 1 or (resid 222 through 224 and (name N or name CA or name C or name O or name C \ B or name H or name HA )) or resid 225 through 230 or (resid 231 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 232 thro \ ugh 234 or (resid 235 and (name N or name CA or name C or name O or name CB or n \ ame H or name HA )) or resid 236 through 237 or (resid 238 and (name N or name C \ A or name C or name O or name CB or name H or name HA )) or resid 239 through 24 \ 3 or (resid 244 through 246 and (name N or name CA or name C or name O or name C \ B or name H or name HA )) or resid 247 through 257 or (resid 258 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 259 thro \ ugh 263 or (resid 264 and (name N or name CA or name C or name O or name CB or n \ ame H or name HA )) or resid 265 through 283 or (resid 284 and (name N or name C \ A or name C or name O or name CB or name H or name HA )) or resid 285 or (resid \ 286 and (name N or name CA or name C or name O or name CB or name H or name HA ) \ ) or resid 287 through 298 or (resid 299 and (name N or name CA or name C or nam \ e O or name CB or name H or name HA )) or resid 300 through 314 or (resid 315 an \ d (name N or name CA or name C or name O or name CB or name HA )) or (resid 316 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 317 through 324 or (resid 325 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 326 through 327 or (resid 328 and (n \ ame N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 329 through 335 or (resid 336 and (name N or name CA or name C or name O or nam \ e CB or name H or name HA )) or resid 337 through 339 or (resid 340 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 341 t \ hrough 366 or (resid 367 through 369 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 370 through 376 or (resid 377 and (n \ ame N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 378 or (resid 379 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 380 through 395 or (resid 396 and (name N or name CA o \ r name C or name O or name CB or name H or name HA )) or resid 397 through 399 o \ r (resid 400 through 401 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 402 through 407 or (resid 408 and (name N or nam \ e CA or name C or name O or name CB or name H or name HA )) or resid 409 through \ 411 or (resid 412 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 413 through 457 or (resid 458 and (name N or name CA o \ r name C or name O or name CB or name H or name HA )) or resid 459 through 460 o \ r (resid 461 through 464 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 465 through 476 or (resid 477 and (name N or nam \ e CA or name C or name O or name CB or name H or name HA )) or resid 478 through \ 483 or (resid 484 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 485 through 489 or (resid 490 and (name N or name CA o \ r name C or name O or name CB or name H or name HA )) or resid 491 through 501 o \ r (resid 502 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 503 through 509 or (resid 529 and (name N or name CA or name \ C or name O or name CB or name OG or name HA or name HB2 or name HB3 or name HG \ )) or (resid 530 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 531 through 540 or (resid 541 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 542 through 549 or \ (resid 550 and (name N or name CA or name C or name O or name CB or name H or n \ ame HA )) or resid 551 through 554 or (resid 555 through 556 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 557 through \ 602 or (resid 603 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 604 through 606 or (resid 607 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 608 or (resid 609 \ through 611 and (name N or name CA or name C or name O or name CB or name H or n \ ame HA )) or resid 612 through 630 or (resid 631 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 632 through 640 or (resi \ d 641 through 643 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 644 or (resid 645 through 646 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 647 through 657 or \ (resid 658 and (name N or name CA or name C or name O or name CB or name H or n \ ame HA )) or resid 659 through 662 or (resid 663 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name C or name O or name CB \ or name HA )) or resid 602 through 603 or (resid 604 and (name N or name CA or n \ ame C or name O or name CB or name H or name HA )) or resid 605 through 611 or ( \ resid 612 and (name N or name CA or name C or name O or name CB or name H or nam \ e HA )) or resid 613 through 617 or (resid 618 through 619 and (name N or name C \ A or name C or name O or name CB or name H or name HA )) or resid 620 through 62 \ 5 or (resid 626 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 630 through 644 or (resid 645 through 646 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 647 thro \ ugh 650 or (resid 651 and (name N or name CA or name C or name O or name CB or n \ ame H or name HA )) or resid 652 through 662 or (resid 663 and (name N or name C \ A or name C or name O or name CB or name H or name HA )) or resid 664 or (resid \ 665 and (name N or name CA or name C or name O or name CB or name H or name HA ) \ ) or resid 666 through 667 or (resid 668 and (name N or name CA or name C or nam \ e O or name CB or name H or name HA )) or resid 669 or resid 680 or (resid 681 a \ nd (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 682 through 683 or (resid 684 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 685 through 693 or (resid 694 through \ 695 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 696 or (resid 697 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 698 through 699 or (resid 700 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 701 th \ rough 706 or (resid 707 through 708 and (name N or name CA or name C or name O o \ r name CB or name HA )) or resid 709 through 713 or (resid 714 through 716 and ( \ name N or name CA or name C or name O or name CB or name H or name HA )) or resi \ d 717 through 729 or (resid 730 through 733 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 734 through 740 or (resid 741 \ through 742 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 743 through 754 or (resid 755 through 756 and (name N or nam \ e CA or name C or name O or name CB or name H or name HA )) or resid 757 through \ 758 or (resid 759 through 760 and (name N or name CA or name C or name O or nam \ e CB or name H or name HA )) or resid 761 through 768 or (resid 769 through 770 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 771 through 773 or (resid 774 through 775 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 776 or resid 801)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.600 Extract box with map and model: 1.290 Check model and map are aligned: 0.230 Set scattering table: 0.280 Process input model: 79.360 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.935 17553 Z= 0.602 Angle : 1.120 53.873 23909 Z= 0.584 Chirality : 0.044 1.073 2964 Planarity : 0.007 0.179 3029 Dihedral : 14.188 88.118 5914 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.25 % Favored : 91.45 % Rotamer: Outliers : 0.37 % Allowed : 4.02 % Favored : 95.62 % Cbeta Deviations : 0.39 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.99 (0.13), residues: 2363 helix: -2.88 (0.09), residues: 1667 sheet: -4.45 (0.57), residues: 8 loop : -3.93 (0.19), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 598 HIS 0.008 0.001 HIS C 746 PHE 0.021 0.002 PHE D 383 TYR 0.010 0.001 TYR B 397 ARG 0.004 0.001 ARG C 702 Details of bonding type rmsd hydrogen bonds : bond 0.14787 ( 1252) hydrogen bonds : angle 7.23206 ( 3687) metal coordination : bond 0.68952 ( 8) metal coordination : angle 28.78616 ( 12) SS BOND : bond 0.01911 ( 5) SS BOND : angle 4.06142 ( 10) covalent geometry : bond 0.00572 (17540) covalent geometry : angle 0.91219 (23887) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 11 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue MET 76 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue ILE 103 is missing expected H atoms. Skipping. Residue SER 115 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Residue SER 129 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue SER 246 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue TYR 361 is missing expected H atoms. Skipping. Residue SER 464 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue MET 489 is missing expected H atoms. Skipping. Residue VAL 496 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue THR 504 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue THR 562 is missing expected H atoms. Skipping. Residue VAL 567 is missing expected H atoms. Skipping. Residue TYR 570 is missing expected H atoms. Skipping. Residue SER 581 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue LEU 587 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue MET 593 is missing expected H atoms. Skipping. Residue LEU 594 is missing expected H atoms. Skipping. Residue SER 595 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue ILE 599 is missing expected H atoms. Skipping. Residue THR 611 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue SER 629 is missing expected H atoms. Skipping. Residue SER 634 is missing expected H atoms. Skipping. Residue TYR 656 is missing expected H atoms. Skipping. Residue LEU 660 is missing expected H atoms. Skipping. Residue SER 662 is missing expected H atoms. Skipping. Residue ILE 677 is missing expected H atoms. Skipping. Residue LEU 679 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue LEU 692 is missing expected H atoms. Skipping. Residue ILE 693 is missing expected H atoms. Skipping. Residue LYS 695 is missing expected H atoms. Skipping. Residue VAL 696 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 704 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue VAL 715 is missing expected H atoms. Skipping. Residue THR 717 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 789 is missing expected H atoms. Skipping. Residue LYS 791 is missing expected H atoms. Skipping. Residue LEU 793 is missing expected H atoms. Skipping. Residue LEU 806 is missing expected H atoms. Skipping. Residue THR 808 is missing expected H atoms. Skipping. Residue LEU 809 is missing expected H atoms. Skipping. Residue SER 825 is missing expected H atoms. Skipping. Residue LYS 829 is missing expected H atoms. Skipping. Residue LYS 851 is missing expected H atoms. Skipping. Residue SER 898 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 920 is missing expected H atoms. Skipping. Residue LYS 921 is missing expected H atoms. Skipping. Residue SER 924 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LYS 931 is missing expected H atoms. Skipping. Residue THR 947 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue THR 64 is missing expected H atoms. Skipping. Residue MET 67 is missing expected H atoms. Skipping. Residue LEU 69 is missing expected H atoms. Skipping. Residue ILE 72 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Residue SER 129 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 196 is missing expected H atoms. Skipping. Residue SER 198 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue ILE 244 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 299 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue MET 328 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue LYS 369 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LEU 379 is missing expected H atoms. Skipping. Residue LEU 396 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue LYS 401 is missing expected H atoms. Skipping. Residue ILE 408 is missing expected H atoms. Skipping. Residue LYS 452 is missing expected H atoms. Skipping. Residue ILE 461 is missing expected H atoms. Skipping. Residue LEU 462 is missing expected H atoms. Skipping. Residue LEU 477 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue LEU 490 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue LEU 502 is missing expected H atoms. Skipping. Residue VAL 530 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue THR 541 is missing expected H atoms. Skipping. Residue LEU 550 is missing expected H atoms. Skipping. Residue LYS 556 is missing expected H atoms. Skipping. Residue THR 562 is missing expected H atoms. Skipping. Residue VAL 567 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue THR 611 is missing expected H atoms. Skipping. Residue SER 634 is missing expected H atoms. Skipping. Residue THR 641 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue TYR 656 is missing expected H atoms. Skipping. Residue LEU 660 is missing expected H atoms. Skipping. Residue SER 662 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue VAL 672 is missing expected H atoms. Skipping. Residue LEU 678 is missing expected H atoms. Skipping. Residue VAL 688 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue LEU 692 is missing expected H atoms. Skipping. Residue ILE 693 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LEU 714 is missing expected H atoms. Skipping. Residue THR 717 is missing expected H atoms. Skipping. Residue MET 721 is missing expected H atoms. Skipping. Residue TYR 723 is missing expected H atoms. Skipping. Residue THR 729 is missing expected H atoms. Skipping. Residue SER 749 is missing expected H atoms. Skipping. Residue SER 754 is missing expected H atoms. Skipping. Residue SER 755 is missing expected H atoms. Skipping. Residue SER 756 is missing expected H atoms. Skipping. Residue LEU 758 is missing expected H atoms. Skipping. Residue SER 761 is missing expected H atoms. Skipping. Residue LYS 771 is missing expected H atoms. Skipping. Residue LYS 772 is missing expected H atoms. Skipping. Residue LYS 773 is missing expected H atoms. Skipping. Residue ILE 774 is missing expected H atoms. Skipping. Residue SER 776 is missing expected H atoms. Skipping. Residue VAL 778 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue LEU 793 is missing expected H atoms. Skipping. Residue THR 808 is missing expected H atoms. Skipping. Residue SER 825 is missing expected H atoms. Skipping. Residue ILE 828 is missing expected H atoms. Skipping. Residue LYS 829 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue LYS 843 is missing expected H atoms. Skipping. Residue VAL 847 is missing expected H atoms. Skipping. Residue LEU 848 is missing expected H atoms. Skipping. Residue LYS 851 is missing expected H atoms. Skipping. Residue TYR 854 is missing expected H atoms. Skipping. Residue ILE 859 is missing expected H atoms. Skipping. Residue THR 872 is missing expected H atoms. Skipping. Residue ILE 876 is missing expected H atoms. Skipping. Residue LYS 881 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LEU 892 is missing expected H atoms. Skipping. Residue LEU 893 is missing expected H atoms. Skipping. Residue LEU 896 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue LYS 921 is missing expected H atoms. Skipping. Residue SER 924 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LYS 931 is missing expected H atoms. Skipping. Residue SER 310 is missing expected H atoms. Skipping. Residue SER 325 is missing expected H atoms. Skipping. Residue SER 328 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue SER 336 is missing expected H atoms. Skipping. Residue SER 373 is missing expected H atoms. Skipping. Residue LEU 375 is missing expected H atoms. Skipping. Residue LEU 410 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue VAL 417 is missing expected H atoms. Skipping. Residue ILE 427 is missing expected H atoms. Skipping. Residue VAL 468 is missing expected H atoms. Skipping. Residue ILE 470 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue MET 541 is missing expected H atoms. Skipping. Residue SER 549 is missing expected H atoms. Skipping. Residue VAL 560 is missing expected H atoms. Skipping. Residue LEU 565 is missing expected H atoms. Skipping. Residue LYS 566 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue VAL 586 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LEU 600 is missing expected H atoms. Skipping. Residue VAL 603 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue LEU 631 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 633 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue SER 641 is missing expected H atoms. Skipping. Residue VAL 646 is missing expected H atoms. Skipping. Residue VAL 659 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 716 is missing expected H atoms. Skipping. Residue LEU 720 is missing expected H atoms. Skipping. Residue LEU 736 is missing expected H atoms. Skipping. Residue MET 738 is missing expected H atoms. Skipping. Residue VAL 742 is missing expected H atoms. Skipping. Residue LEU 745 is missing expected H atoms. Skipping. Residue MET 752 is missing expected H atoms. Skipping. Residue LEU 762 is missing expected H atoms. Skipping. Residue ALA 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue LEU 375 is missing expected H atoms. Skipping. Residue LEU 410 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue VAL 417 is missing expected H atoms. Skipping. Residue VAL 423 is missing expected H atoms. Skipping. Residue ALA 433 is missing expected H atoms. Skipping. Residue LEU 437 is missing expected H atoms. Skipping. Residue SER 467 is missing expected H atoms. Skipping. Residue VAL 468 is missing expected H atoms. Skipping. Residue ILE 470 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue ILE 481 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue LEU 495 is missing expected H atoms. Skipping. Residue LEU 496 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue VAL 560 is missing expected H atoms. Skipping. Residue LEU 565 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue VAL 569 is missing expected H atoms. Skipping. Residue LEU 571 is missing expected H atoms. Skipping. Residue SER 576 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue SER 595 is missing expected H atoms. Skipping. Residue THR 598 is missing expected H atoms. Skipping. Residue LEU 600 is missing expected H atoms. Skipping. Residue LEU 604 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue SER 641 is missing expected H atoms. Skipping. Residue LEU 663 is missing expected H atoms. Skipping. Residue LYS 665 is missing expected H atoms. Skipping. Residue VAL 668 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 694 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 700 is missing expected H atoms. Skipping. Residue LEU 730 is missing expected H atoms. Skipping. Residue SER 731 is missing expected H atoms. Skipping. Residue LYS 733 is missing expected H atoms. Skipping. Residue MET 738 is missing expected H atoms. Skipping. Residue VAL 755 is missing expected H atoms. Skipping. Residue SER 756 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ALA 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Evaluate side-chains 236 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 230 time to evaluate : 2.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 MET cc_start: 0.7193 (mmt) cc_final: 0.6734 (mmt) REVERT: D 377 GLU cc_start: 0.7106 (tm-30) cc_final: 0.6691 (tm-30) REVERT: C 636 TYR cc_start: 0.8313 (m-10) cc_final: 0.8071 (m-10) REVERT: C 685 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7880 (tm-30) REVERT: C 752 MET cc_start: 0.8274 (tpt) cc_final: 0.7984 (tpp) outliers start: 6 outliers final: 2 residues processed: 235 average time/residue: 0.5974 time to fit residues: 213.8754 Evaluate side-chains 169 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 167 time to evaluate : 2.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 630 CYS Chi-restraints excluded: chain C residue 680 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 201 optimal weight: 0.6980 chunk 181 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 122 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 187 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 217 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 681 GLN D 483 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.101430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.079565 restraints weight = 156996.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.082589 restraints weight = 74367.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.084446 restraints weight = 47560.642| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 17553 Z= 0.215 Angle : 0.831 50.641 23909 Z= 0.372 Chirality : 0.039 0.462 2964 Planarity : 0.005 0.068 3029 Dihedral : 5.442 45.743 2481 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.36 % Favored : 92.55 % Rotamer: Outliers : 1.16 % Allowed : 8.89 % Favored : 89.96 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.16), residues: 2363 helix: -1.07 (0.11), residues: 1723 sheet: -4.43 (0.64), residues: 8 loop : -3.04 (0.22), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 598 HIS 0.007 0.001 HIS A 664 PHE 0.015 0.001 PHE D 383 TYR 0.015 0.001 TYR B 908 ARG 0.010 0.001 ARG D 645 Details of bonding type rmsd hydrogen bonds : bond 0.05434 ( 1252) hydrogen bonds : angle 5.78702 ( 3687) metal coordination : bond 0.03353 ( 8) metal coordination : angle 22.55452 ( 12) SS BOND : bond 0.00823 ( 5) SS BOND : angle 4.35757 ( 10) covalent geometry : bond 0.00455 (17540) covalent geometry : angle 0.65372 (23887) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 11 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue MET 76 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue ILE 103 is missing expected H atoms. Skipping. Residue SER 115 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Residue SER 129 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue SER 246 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue TYR 361 is missing expected H atoms. Skipping. Residue SER 464 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue MET 489 is missing expected H atoms. Skipping. Residue VAL 496 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue THR 504 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue THR 562 is missing expected H atoms. Skipping. Residue VAL 567 is missing expected H atoms. Skipping. Residue TYR 570 is missing expected H atoms. Skipping. Residue SER 581 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue LEU 587 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue MET 593 is missing expected H atoms. Skipping. Residue LEU 594 is missing expected H atoms. Skipping. Residue SER 595 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue ILE 599 is missing expected H atoms. Skipping. Residue THR 611 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue SER 629 is missing expected H atoms. Skipping. Residue SER 634 is missing expected H atoms. Skipping. Residue TYR 656 is missing expected H atoms. Skipping. Residue LEU 660 is missing expected H atoms. Skipping. Residue SER 662 is missing expected H atoms. Skipping. Residue ILE 677 is missing expected H atoms. Skipping. Residue LEU 679 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue LEU 692 is missing expected H atoms. Skipping. Residue ILE 693 is missing expected H atoms. Skipping. Residue LYS 695 is missing expected H atoms. Skipping. Residue VAL 696 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 704 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue VAL 715 is missing expected H atoms. Skipping. Residue THR 717 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 789 is missing expected H atoms. Skipping. Residue LYS 791 is missing expected H atoms. Skipping. Residue LEU 793 is missing expected H atoms. Skipping. Residue LEU 806 is missing expected H atoms. Skipping. Residue THR 808 is missing expected H atoms. Skipping. Residue LEU 809 is missing expected H atoms. Skipping. Residue SER 825 is missing expected H atoms. Skipping. Residue LYS 829 is missing expected H atoms. Skipping. Residue LYS 851 is missing expected H atoms. Skipping. Residue SER 898 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 920 is missing expected H atoms. Skipping. Residue LYS 921 is missing expected H atoms. Skipping. Residue SER 924 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LYS 931 is missing expected H atoms. Skipping. Residue THR 947 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue THR 64 is missing expected H atoms. Skipping. Residue MET 67 is missing expected H atoms. Skipping. Residue LEU 69 is missing expected H atoms. Skipping. Residue ILE 72 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Residue SER 129 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 196 is missing expected H atoms. Skipping. Residue SER 198 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue ILE 244 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 299 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue MET 328 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue LYS 369 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LEU 379 is missing expected H atoms. Skipping. Residue LEU 396 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue LYS 401 is missing expected H atoms. Skipping. Residue ILE 408 is missing expected H atoms. Skipping. Residue LYS 452 is missing expected H atoms. Skipping. Residue ILE 461 is missing expected H atoms. Skipping. Residue LEU 462 is missing expected H atoms. Skipping. Residue LEU 477 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue LEU 490 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue LEU 502 is missing expected H atoms. Skipping. Residue VAL 530 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue THR 541 is missing expected H atoms. Skipping. Residue LEU 550 is missing expected H atoms. Skipping. Residue LYS 556 is missing expected H atoms. Skipping. Residue THR 562 is missing expected H atoms. Skipping. Residue VAL 567 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue THR 611 is missing expected H atoms. Skipping. Residue SER 634 is missing expected H atoms. Skipping. Residue THR 641 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue TYR 656 is missing expected H atoms. Skipping. Residue LEU 660 is missing expected H atoms. Skipping. Residue SER 662 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue VAL 672 is missing expected H atoms. Skipping. Residue LEU 678 is missing expected H atoms. Skipping. Residue VAL 688 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue LEU 692 is missing expected H atoms. Skipping. Residue ILE 693 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LEU 714 is missing expected H atoms. Skipping. Residue THR 717 is missing expected H atoms. Skipping. Residue MET 721 is missing expected H atoms. Skipping. Residue TYR 723 is missing expected H atoms. Skipping. Residue THR 729 is missing expected H atoms. Skipping. Residue SER 749 is missing expected H atoms. Skipping. Residue SER 754 is missing expected H atoms. Skipping. Residue SER 755 is missing expected H atoms. Skipping. Residue SER 756 is missing expected H atoms. Skipping. Residue LEU 758 is missing expected H atoms. Skipping. Residue SER 761 is missing expected H atoms. Skipping. Residue LYS 771 is missing expected H atoms. Skipping. Residue LYS 772 is missing expected H atoms. Skipping. Residue LYS 773 is missing expected H atoms. Skipping. Residue ILE 774 is missing expected H atoms. Skipping. Residue SER 776 is missing expected H atoms. Skipping. Residue VAL 778 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue LEU 793 is missing expected H atoms. Skipping. Residue THR 808 is missing expected H atoms. Skipping. Residue SER 825 is missing expected H atoms. Skipping. Residue ILE 828 is missing expected H atoms. Skipping. Residue LYS 829 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue LYS 843 is missing expected H atoms. Skipping. Residue VAL 847 is missing expected H atoms. Skipping. Residue LEU 848 is missing expected H atoms. Skipping. Residue LYS 851 is missing expected H atoms. Skipping. Residue TYR 854 is missing expected H atoms. Skipping. Residue ILE 859 is missing expected H atoms. Skipping. Residue THR 872 is missing expected H atoms. Skipping. Residue ILE 876 is missing expected H atoms. Skipping. Residue LYS 881 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LEU 892 is missing expected H atoms. Skipping. Residue LEU 893 is missing expected H atoms. Skipping. Residue LEU 896 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue LYS 921 is missing expected H atoms. Skipping. Residue SER 924 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LYS 931 is missing expected H atoms. Skipping. Residue SER 310 is missing expected H atoms. Skipping. Residue SER 325 is missing expected H atoms. Skipping. Residue SER 328 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue SER 336 is missing expected H atoms. Skipping. Residue SER 373 is missing expected H atoms. Skipping. Residue LEU 375 is missing expected H atoms. Skipping. Residue LEU 410 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue VAL 417 is missing expected H atoms. Skipping. Residue ILE 427 is missing expected H atoms. Skipping. Residue VAL 468 is missing expected H atoms. Skipping. Residue ILE 470 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue MET 541 is missing expected H atoms. Skipping. Residue SER 549 is missing expected H atoms. Skipping. Residue VAL 560 is missing expected H atoms. Skipping. Residue LEU 565 is missing expected H atoms. Skipping. Residue LYS 566 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue VAL 586 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LEU 600 is missing expected H atoms. Skipping. Residue VAL 603 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue LEU 631 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 633 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue SER 641 is missing expected H atoms. Skipping. Residue VAL 646 is missing expected H atoms. Skipping. Residue VAL 659 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 716 is missing expected H atoms. Skipping. Residue LEU 720 is missing expected H atoms. Skipping. Residue LEU 736 is missing expected H atoms. Skipping. Residue MET 738 is missing expected H atoms. Skipping. Residue VAL 742 is missing expected H atoms. Skipping. Residue LEU 745 is missing expected H atoms. Skipping. Residue MET 752 is missing expected H atoms. Skipping. Residue LEU 762 is missing expected H atoms. Skipping. Residue ALA 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue LEU 375 is missing expected H atoms. Skipping. Residue LEU 410 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue VAL 417 is missing expected H atoms. Skipping. Residue VAL 423 is missing expected H atoms. Skipping. Residue ALA 433 is missing expected H atoms. Skipping. Residue LEU 437 is missing expected H atoms. Skipping. Residue SER 467 is missing expected H atoms. Skipping. Residue VAL 468 is missing expected H atoms. Skipping. Residue ILE 470 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue ILE 481 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue LEU 495 is missing expected H atoms. Skipping. Residue LEU 496 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue VAL 560 is missing expected H atoms. Skipping. Residue LEU 565 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue VAL 569 is missing expected H atoms. Skipping. Residue LEU 571 is missing expected H atoms. Skipping. Residue SER 576 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue SER 595 is missing expected H atoms. Skipping. Residue THR 598 is missing expected H atoms. Skipping. Residue LEU 600 is missing expected H atoms. Skipping. Residue LEU 604 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue SER 641 is missing expected H atoms. Skipping. Residue LEU 663 is missing expected H atoms. Skipping. Residue LYS 665 is missing expected H atoms. Skipping. Residue VAL 668 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 694 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 700 is missing expected H atoms. Skipping. Residue LEU 730 is missing expected H atoms. Skipping. Residue SER 731 is missing expected H atoms. Skipping. Residue LYS 733 is missing expected H atoms. Skipping. Residue MET 738 is missing expected H atoms. Skipping. Residue VAL 755 is missing expected H atoms. Skipping. Residue SER 756 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ALA 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Evaluate side-chains 205 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 186 time to evaluate : 3.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 377 GLU cc_start: 0.7355 (tm-30) cc_final: 0.7073 (tm-30) REVERT: C 680 CYS cc_start: 0.6983 (OUTLIER) cc_final: 0.6725 (t) REVERT: C 685 GLU cc_start: 0.8347 (tm-30) cc_final: 0.8139 (tm-30) REVERT: C 749 ASP cc_start: 0.8646 (m-30) cc_final: 0.8235 (m-30) REVERT: C 767 ASP cc_start: 0.7496 (t70) cc_final: 0.7274 (t70) outliers start: 19 outliers final: 10 residues processed: 201 average time/residue: 0.5814 time to fit residues: 181.7331 Evaluate side-chains 171 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 160 time to evaluate : 2.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 925 PHE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 908 TYR Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 680 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 34 optimal weight: 3.9990 chunk 114 optimal weight: 0.0670 chunk 208 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 160 optimal weight: 6.9990 chunk 220 optimal weight: 4.9990 chunk 210 optimal weight: 0.6980 chunk 189 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 chunk 87 optimal weight: 2.9990 overall best weight: 1.9524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.101619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.079410 restraints weight = 155518.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.082428 restraints weight = 74184.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.084291 restraints weight = 47546.949| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 17553 Z= 0.165 Angle : 0.752 44.762 23909 Z= 0.328 Chirality : 0.037 0.456 2964 Planarity : 0.005 0.070 3029 Dihedral : 4.998 54.575 2480 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.56 % Favored : 93.36 % Rotamer: Outliers : 1.16 % Allowed : 10.59 % Favored : 88.25 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.17), residues: 2363 helix: 0.17 (0.12), residues: 1731 sheet: -4.28 (0.73), residues: 8 loop : -2.52 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 598 HIS 0.007 0.001 HIS C 488 PHE 0.017 0.001 PHE A 925 TYR 0.013 0.001 TYR C 636 ARG 0.003 0.000 ARG B 223 Details of bonding type rmsd hydrogen bonds : bond 0.04857 ( 1252) hydrogen bonds : angle 5.25132 ( 3687) metal coordination : bond 0.01465 ( 8) metal coordination : angle 21.12324 ( 12) SS BOND : bond 0.01455 ( 5) SS BOND : angle 3.88062 ( 10) covalent geometry : bond 0.00344 (17540) covalent geometry : angle 0.57973 (23887) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 11 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue MET 76 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue ILE 103 is missing expected H atoms. Skipping. Residue SER 115 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Residue SER 129 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue SER 246 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue TYR 361 is missing expected H atoms. Skipping. Residue SER 464 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue MET 489 is missing expected H atoms. Skipping. Residue VAL 496 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue THR 504 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue THR 562 is missing expected H atoms. Skipping. Residue VAL 567 is missing expected H atoms. Skipping. Residue TYR 570 is missing expected H atoms. Skipping. Residue SER 581 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue LEU 587 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue MET 593 is missing expected H atoms. Skipping. Residue LEU 594 is missing expected H atoms. Skipping. Residue SER 595 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue ILE 599 is missing expected H atoms. Skipping. Residue THR 611 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue SER 629 is missing expected H atoms. Skipping. Residue SER 634 is missing expected H atoms. Skipping. Residue TYR 656 is missing expected H atoms. Skipping. Residue LEU 660 is missing expected H atoms. Skipping. Residue SER 662 is missing expected H atoms. Skipping. Residue ILE 677 is missing expected H atoms. Skipping. Residue LEU 679 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue LEU 692 is missing expected H atoms. Skipping. Residue ILE 693 is missing expected H atoms. Skipping. Residue LYS 695 is missing expected H atoms. Skipping. Residue VAL 696 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 704 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue VAL 715 is missing expected H atoms. Skipping. Residue THR 717 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 789 is missing expected H atoms. Skipping. Residue LYS 791 is missing expected H atoms. Skipping. Residue LEU 793 is missing expected H atoms. Skipping. Residue LEU 806 is missing expected H atoms. Skipping. Residue THR 808 is missing expected H atoms. Skipping. Residue LEU 809 is missing expected H atoms. Skipping. Residue SER 825 is missing expected H atoms. Skipping. Residue LYS 829 is missing expected H atoms. Skipping. Residue LYS 851 is missing expected H atoms. Skipping. Residue SER 898 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 920 is missing expected H atoms. Skipping. Residue LYS 921 is missing expected H atoms. Skipping. Residue SER 924 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LYS 931 is missing expected H atoms. Skipping. Residue THR 947 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue THR 64 is missing expected H atoms. Skipping. Residue MET 67 is missing expected H atoms. Skipping. Residue LEU 69 is missing expected H atoms. Skipping. Residue ILE 72 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Residue SER 129 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 196 is missing expected H atoms. Skipping. Residue SER 198 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue ILE 244 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 299 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue MET 328 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue LYS 369 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LEU 379 is missing expected H atoms. Skipping. Residue LEU 396 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue LYS 401 is missing expected H atoms. Skipping. Residue ILE 408 is missing expected H atoms. Skipping. Residue LYS 452 is missing expected H atoms. Skipping. Residue ILE 461 is missing expected H atoms. Skipping. Residue LEU 462 is missing expected H atoms. Skipping. Residue LEU 477 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue LEU 490 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue LEU 502 is missing expected H atoms. Skipping. Residue VAL 530 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue THR 541 is missing expected H atoms. Skipping. Residue LEU 550 is missing expected H atoms. Skipping. Residue LYS 556 is missing expected H atoms. Skipping. Residue THR 562 is missing expected H atoms. Skipping. Residue VAL 567 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue THR 611 is missing expected H atoms. Skipping. Residue SER 634 is missing expected H atoms. Skipping. Residue THR 641 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue TYR 656 is missing expected H atoms. Skipping. Residue LEU 660 is missing expected H atoms. Skipping. Residue SER 662 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue VAL 672 is missing expected H atoms. Skipping. Residue LEU 678 is missing expected H atoms. Skipping. Residue VAL 688 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue LEU 692 is missing expected H atoms. Skipping. Residue ILE 693 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LEU 714 is missing expected H atoms. Skipping. Residue THR 717 is missing expected H atoms. Skipping. Residue MET 721 is missing expected H atoms. Skipping. Residue TYR 723 is missing expected H atoms. Skipping. Residue THR 729 is missing expected H atoms. Skipping. Residue SER 749 is missing expected H atoms. Skipping. Residue SER 754 is missing expected H atoms. Skipping. Residue SER 755 is missing expected H atoms. Skipping. Residue SER 756 is missing expected H atoms. Skipping. Residue LEU 758 is missing expected H atoms. Skipping. Residue SER 761 is missing expected H atoms. Skipping. Residue LYS 771 is missing expected H atoms. Skipping. Residue LYS 772 is missing expected H atoms. Skipping. Residue LYS 773 is missing expected H atoms. Skipping. Residue ILE 774 is missing expected H atoms. Skipping. Residue SER 776 is missing expected H atoms. Skipping. Residue VAL 778 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue LEU 793 is missing expected H atoms. Skipping. Residue THR 808 is missing expected H atoms. Skipping. Residue SER 825 is missing expected H atoms. Skipping. Residue ILE 828 is missing expected H atoms. Skipping. Residue LYS 829 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue LYS 843 is missing expected H atoms. Skipping. Residue VAL 847 is missing expected H atoms. Skipping. Residue LEU 848 is missing expected H atoms. Skipping. Residue LYS 851 is missing expected H atoms. Skipping. Residue TYR 854 is missing expected H atoms. Skipping. Residue ILE 859 is missing expected H atoms. Skipping. Residue THR 872 is missing expected H atoms. Skipping. Residue ILE 876 is missing expected H atoms. Skipping. Residue LYS 881 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LEU 892 is missing expected H atoms. Skipping. Residue LEU 893 is missing expected H atoms. Skipping. Residue LEU 896 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue LYS 921 is missing expected H atoms. Skipping. Residue SER 924 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LYS 931 is missing expected H atoms. Skipping. Residue SER 310 is missing expected H atoms. Skipping. Residue SER 325 is missing expected H atoms. Skipping. Residue SER 328 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue SER 336 is missing expected H atoms. Skipping. Residue SER 373 is missing expected H atoms. Skipping. Residue LEU 375 is missing expected H atoms. Skipping. Residue LEU 410 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue VAL 417 is missing expected H atoms. Skipping. Residue ILE 427 is missing expected H atoms. Skipping. Residue VAL 468 is missing expected H atoms. Skipping. Residue ILE 470 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue MET 541 is missing expected H atoms. Skipping. Residue SER 549 is missing expected H atoms. Skipping. Residue VAL 560 is missing expected H atoms. Skipping. Residue LEU 565 is missing expected H atoms. Skipping. Residue LYS 566 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue VAL 586 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LEU 600 is missing expected H atoms. Skipping. Residue VAL 603 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue LEU 631 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 633 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue SER 641 is missing expected H atoms. Skipping. Residue VAL 646 is missing expected H atoms. Skipping. Residue VAL 659 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 716 is missing expected H atoms. Skipping. Residue LEU 720 is missing expected H atoms. Skipping. Residue LEU 736 is missing expected H atoms. Skipping. Residue MET 738 is missing expected H atoms. Skipping. Residue VAL 742 is missing expected H atoms. Skipping. Residue LEU 745 is missing expected H atoms. Skipping. Residue MET 752 is missing expected H atoms. Skipping. Residue LEU 762 is missing expected H atoms. Skipping. Residue ALA 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue LEU 375 is missing expected H atoms. Skipping. Residue LEU 410 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue VAL 417 is missing expected H atoms. Skipping. Residue VAL 423 is missing expected H atoms. Skipping. Residue ALA 433 is missing expected H atoms. Skipping. Residue LEU 437 is missing expected H atoms. Skipping. Residue SER 467 is missing expected H atoms. Skipping. Residue VAL 468 is missing expected H atoms. Skipping. Residue ILE 470 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue ILE 481 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue LEU 495 is missing expected H atoms. Skipping. Residue LEU 496 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue VAL 560 is missing expected H atoms. Skipping. Residue LEU 565 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue VAL 569 is missing expected H atoms. Skipping. Residue LEU 571 is missing expected H atoms. Skipping. Residue SER 576 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue SER 595 is missing expected H atoms. Skipping. Residue THR 598 is missing expected H atoms. Skipping. Residue LEU 600 is missing expected H atoms. Skipping. Residue LEU 604 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue SER 641 is missing expected H atoms. Skipping. Residue LEU 663 is missing expected H atoms. Skipping. Residue LYS 665 is missing expected H atoms. Skipping. Residue VAL 668 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 694 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 700 is missing expected H atoms. Skipping. Residue LEU 730 is missing expected H atoms. Skipping. Residue SER 731 is missing expected H atoms. Skipping. Residue LYS 733 is missing expected H atoms. Skipping. Residue MET 738 is missing expected H atoms. Skipping. Residue VAL 755 is missing expected H atoms. Skipping. Residue SER 756 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ALA 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Evaluate side-chains 202 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 183 time to evaluate : 2.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 MET cc_start: 0.7114 (mmt) cc_final: 0.6671 (mmt) REVERT: D 377 GLU cc_start: 0.7358 (tm-30) cc_final: 0.7103 (tm-30) REVERT: D 638 TYR cc_start: 0.8778 (t80) cc_final: 0.8540 (t80) REVERT: D 767 ASP cc_start: 0.7466 (t70) cc_final: 0.7124 (t70) REVERT: C 749 ASP cc_start: 0.8636 (m-30) cc_final: 0.8317 (m-30) REVERT: C 767 ASP cc_start: 0.7501 (t70) cc_final: 0.7262 (t70) outliers start: 19 outliers final: 10 residues processed: 196 average time/residue: 0.5380 time to fit residues: 168.3983 Evaluate side-chains 183 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 173 time to evaluate : 3.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 925 PHE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 908 TYR Chi-restraints excluded: chain C residue 471 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 185 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 160 optimal weight: 4.9990 chunk 143 optimal weight: 0.9980 chunk 218 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 0.5980 chunk 229 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 392 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.101214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.079007 restraints weight = 156065.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.081916 restraints weight = 74816.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.083755 restraints weight = 48348.590| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 17553 Z= 0.171 Angle : 0.744 43.232 23909 Z= 0.325 Chirality : 0.037 0.459 2964 Planarity : 0.005 0.071 3029 Dihedral : 4.712 37.903 2479 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.64 % Favored : 93.27 % Rotamer: Outliers : 1.16 % Allowed : 11.87 % Favored : 86.98 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.18), residues: 2363 helix: 0.69 (0.13), residues: 1734 sheet: -4.14 (0.74), residues: 8 loop : -2.29 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 652 HIS 0.008 0.001 HIS B 509 PHE 0.016 0.001 PHE A 925 TYR 0.012 0.001 TYR C 636 ARG 0.002 0.000 ARG B 223 Details of bonding type rmsd hydrogen bonds : bond 0.04515 ( 1252) hydrogen bonds : angle 5.04828 ( 3687) metal coordination : bond 0.01383 ( 8) metal coordination : angle 20.58182 ( 12) SS BOND : bond 0.01014 ( 5) SS BOND : angle 4.21655 ( 10) covalent geometry : bond 0.00360 (17540) covalent geometry : angle 0.57815 (23887) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 11 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue MET 76 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue ILE 103 is missing expected H atoms. Skipping. Residue SER 115 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Residue SER 129 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue SER 246 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue TYR 361 is missing expected H atoms. Skipping. Residue SER 464 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue MET 489 is missing expected H atoms. Skipping. Residue VAL 496 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue THR 504 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue THR 562 is missing expected H atoms. Skipping. Residue VAL 567 is missing expected H atoms. Skipping. Residue TYR 570 is missing expected H atoms. Skipping. Residue SER 581 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue LEU 587 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue MET 593 is missing expected H atoms. Skipping. Residue LEU 594 is missing expected H atoms. Skipping. Residue SER 595 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue ILE 599 is missing expected H atoms. Skipping. Residue THR 611 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue SER 629 is missing expected H atoms. Skipping. Residue SER 634 is missing expected H atoms. Skipping. Residue TYR 656 is missing expected H atoms. Skipping. Residue LEU 660 is missing expected H atoms. Skipping. Residue SER 662 is missing expected H atoms. Skipping. Residue ILE 677 is missing expected H atoms. Skipping. Residue LEU 679 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue LEU 692 is missing expected H atoms. Skipping. Residue ILE 693 is missing expected H atoms. Skipping. Residue LYS 695 is missing expected H atoms. Skipping. Residue VAL 696 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 704 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue VAL 715 is missing expected H atoms. Skipping. Residue THR 717 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 789 is missing expected H atoms. Skipping. Residue LYS 791 is missing expected H atoms. Skipping. Residue LEU 793 is missing expected H atoms. Skipping. Residue LEU 806 is missing expected H atoms. Skipping. Residue THR 808 is missing expected H atoms. Skipping. Residue LEU 809 is missing expected H atoms. Skipping. Residue SER 825 is missing expected H atoms. Skipping. Residue LYS 829 is missing expected H atoms. Skipping. Residue LYS 851 is missing expected H atoms. Skipping. Residue SER 898 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 920 is missing expected H atoms. Skipping. Residue LYS 921 is missing expected H atoms. Skipping. Residue SER 924 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LYS 931 is missing expected H atoms. Skipping. Residue THR 947 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue THR 64 is missing expected H atoms. Skipping. Residue MET 67 is missing expected H atoms. Skipping. Residue LEU 69 is missing expected H atoms. Skipping. Residue ILE 72 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Residue SER 129 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 196 is missing expected H atoms. Skipping. Residue SER 198 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue ILE 244 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 299 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue MET 328 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue LYS 369 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LEU 379 is missing expected H atoms. Skipping. Residue LEU 396 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue LYS 401 is missing expected H atoms. Skipping. Residue ILE 408 is missing expected H atoms. Skipping. Residue LYS 452 is missing expected H atoms. Skipping. Residue ILE 461 is missing expected H atoms. Skipping. Residue LEU 462 is missing expected H atoms. Skipping. Residue LEU 477 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue LEU 490 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue LEU 502 is missing expected H atoms. Skipping. Residue VAL 530 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue THR 541 is missing expected H atoms. Skipping. Residue LEU 550 is missing expected H atoms. Skipping. Residue LYS 556 is missing expected H atoms. Skipping. Residue THR 562 is missing expected H atoms. Skipping. Residue VAL 567 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue THR 611 is missing expected H atoms. Skipping. Residue SER 634 is missing expected H atoms. Skipping. Residue THR 641 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue TYR 656 is missing expected H atoms. Skipping. Residue LEU 660 is missing expected H atoms. Skipping. Residue SER 662 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue VAL 672 is missing expected H atoms. Skipping. Residue LEU 678 is missing expected H atoms. Skipping. Residue VAL 688 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue LEU 692 is missing expected H atoms. Skipping. Residue ILE 693 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LEU 714 is missing expected H atoms. Skipping. Residue THR 717 is missing expected H atoms. Skipping. Residue MET 721 is missing expected H atoms. Skipping. Residue TYR 723 is missing expected H atoms. Skipping. Residue THR 729 is missing expected H atoms. Skipping. Residue SER 749 is missing expected H atoms. Skipping. Residue SER 754 is missing expected H atoms. Skipping. Residue SER 755 is missing expected H atoms. Skipping. Residue SER 756 is missing expected H atoms. Skipping. Residue LEU 758 is missing expected H atoms. Skipping. Residue SER 761 is missing expected H atoms. Skipping. Residue LYS 771 is missing expected H atoms. Skipping. Residue LYS 772 is missing expected H atoms. Skipping. Residue LYS 773 is missing expected H atoms. Skipping. Residue ILE 774 is missing expected H atoms. Skipping. Residue SER 776 is missing expected H atoms. Skipping. Residue VAL 778 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue LEU 793 is missing expected H atoms. Skipping. Residue THR 808 is missing expected H atoms. Skipping. Residue SER 825 is missing expected H atoms. Skipping. Residue ILE 828 is missing expected H atoms. Skipping. Residue LYS 829 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue LYS 843 is missing expected H atoms. Skipping. Residue VAL 847 is missing expected H atoms. Skipping. Residue LEU 848 is missing expected H atoms. Skipping. Residue LYS 851 is missing expected H atoms. Skipping. Residue TYR 854 is missing expected H atoms. Skipping. Residue ILE 859 is missing expected H atoms. Skipping. Residue THR 872 is missing expected H atoms. Skipping. Residue ILE 876 is missing expected H atoms. Skipping. Residue LYS 881 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LEU 892 is missing expected H atoms. Skipping. Residue LEU 893 is missing expected H atoms. Skipping. Residue LEU 896 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue LYS 921 is missing expected H atoms. Skipping. Residue SER 924 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LYS 931 is missing expected H atoms. Skipping. Residue SER 310 is missing expected H atoms. Skipping. Residue SER 325 is missing expected H atoms. Skipping. Residue SER 328 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue SER 336 is missing expected H atoms. Skipping. Residue SER 373 is missing expected H atoms. Skipping. Residue LEU 375 is missing expected H atoms. Skipping. Residue LEU 410 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue VAL 417 is missing expected H atoms. Skipping. Residue ILE 427 is missing expected H atoms. Skipping. Residue VAL 468 is missing expected H atoms. Skipping. Residue ILE 470 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue MET 541 is missing expected H atoms. Skipping. Residue SER 549 is missing expected H atoms. Skipping. Residue VAL 560 is missing expected H atoms. Skipping. Residue LEU 565 is missing expected H atoms. Skipping. Residue LYS 566 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue VAL 586 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LEU 600 is missing expected H atoms. Skipping. Residue VAL 603 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue LEU 631 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 633 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue SER 641 is missing expected H atoms. Skipping. Residue VAL 646 is missing expected H atoms. Skipping. Residue VAL 659 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 716 is missing expected H atoms. Skipping. Residue LEU 720 is missing expected H atoms. Skipping. Residue LEU 736 is missing expected H atoms. Skipping. Residue MET 738 is missing expected H atoms. Skipping. Residue VAL 742 is missing expected H atoms. Skipping. Residue LEU 745 is missing expected H atoms. Skipping. Residue MET 752 is missing expected H atoms. Skipping. Residue LEU 762 is missing expected H atoms. Skipping. Residue ALA 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue LEU 375 is missing expected H atoms. Skipping. Residue LEU 410 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue VAL 417 is missing expected H atoms. Skipping. Residue VAL 423 is missing expected H atoms. Skipping. Residue ALA 433 is missing expected H atoms. Skipping. Residue LEU 437 is missing expected H atoms. Skipping. Residue SER 467 is missing expected H atoms. Skipping. Residue VAL 468 is missing expected H atoms. Skipping. Residue ILE 470 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue ILE 481 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue LEU 495 is missing expected H atoms. Skipping. Residue LEU 496 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue VAL 560 is missing expected H atoms. Skipping. Residue LEU 565 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue VAL 569 is missing expected H atoms. Skipping. Residue LEU 571 is missing expected H atoms. Skipping. Residue SER 576 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue SER 595 is missing expected H atoms. Skipping. Residue THR 598 is missing expected H atoms. Skipping. Residue LEU 600 is missing expected H atoms. Skipping. Residue LEU 604 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue SER 641 is missing expected H atoms. Skipping. Residue LEU 663 is missing expected H atoms. Skipping. Residue LYS 665 is missing expected H atoms. Skipping. Residue VAL 668 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 694 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 700 is missing expected H atoms. Skipping. Residue LEU 730 is missing expected H atoms. Skipping. Residue SER 731 is missing expected H atoms. Skipping. Residue LYS 733 is missing expected H atoms. Skipping. Residue MET 738 is missing expected H atoms. Skipping. Residue VAL 755 is missing expected H atoms. Skipping. Residue SER 756 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ALA 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Evaluate side-chains 200 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 2.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 377 GLU cc_start: 0.7449 (tm-30) cc_final: 0.7213 (tm-30) REVERT: C 548 PHE cc_start: 0.7838 (m-10) cc_final: 0.7566 (m-80) REVERT: C 749 ASP cc_start: 0.8652 (m-30) cc_final: 0.8382 (m-30) REVERT: C 767 ASP cc_start: 0.7501 (t70) cc_final: 0.7234 (t70) outliers start: 19 outliers final: 12 residues processed: 194 average time/residue: 0.5631 time to fit residues: 174.2719 Evaluate side-chains 181 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 169 time to evaluate : 2.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 925 PHE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 908 TYR Chi-restraints excluded: chain C residue 392 ASN Chi-restraints excluded: chain C residue 411 CYS Chi-restraints excluded: chain C residue 471 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 101 optimal weight: 2.9990 chunk 231 optimal weight: 3.9990 chunk 172 optimal weight: 0.9990 chunk 8 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 180 optimal weight: 8.9990 chunk 236 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 193 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.100335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.078193 restraints weight = 154756.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.081133 restraints weight = 72216.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.082913 restraints weight = 45981.507| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 17553 Z= 0.159 Angle : 0.717 42.737 23909 Z= 0.313 Chirality : 0.036 0.459 2964 Planarity : 0.004 0.070 3029 Dihedral : 4.618 37.146 2479 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.18 % Favored : 93.74 % Rotamer: Outliers : 1.16 % Allowed : 12.90 % Favored : 85.94 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.18), residues: 2363 helix: 0.96 (0.13), residues: 1734 sheet: -4.06 (0.75), residues: 8 loop : -2.19 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 598 HIS 0.003 0.001 HIS C 488 PHE 0.018 0.001 PHE A 925 TYR 0.014 0.001 TYR C 636 ARG 0.001 0.000 ARG B 109 Details of bonding type rmsd hydrogen bonds : bond 0.04373 ( 1252) hydrogen bonds : angle 4.92112 ( 3687) metal coordination : bond 0.00998 ( 8) metal coordination : angle 20.05450 ( 12) SS BOND : bond 0.01071 ( 5) SS BOND : angle 3.83524 ( 10) covalent geometry : bond 0.00333 (17540) covalent geometry : angle 0.55302 (23887) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 11 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue MET 76 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue ILE 103 is missing expected H atoms. Skipping. Residue SER 115 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Residue SER 129 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue SER 246 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue TYR 361 is missing expected H atoms. Skipping. Residue SER 464 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue MET 489 is missing expected H atoms. Skipping. Residue VAL 496 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue THR 504 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue THR 562 is missing expected H atoms. Skipping. Residue VAL 567 is missing expected H atoms. Skipping. Residue TYR 570 is missing expected H atoms. Skipping. Residue SER 581 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue LEU 587 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue MET 593 is missing expected H atoms. Skipping. Residue LEU 594 is missing expected H atoms. Skipping. Residue SER 595 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue ILE 599 is missing expected H atoms. Skipping. Residue THR 611 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue SER 629 is missing expected H atoms. Skipping. Residue SER 634 is missing expected H atoms. Skipping. Residue TYR 656 is missing expected H atoms. Skipping. Residue LEU 660 is missing expected H atoms. Skipping. Residue SER 662 is missing expected H atoms. Skipping. Residue ILE 677 is missing expected H atoms. Skipping. Residue LEU 679 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue LEU 692 is missing expected H atoms. Skipping. Residue ILE 693 is missing expected H atoms. Skipping. Residue LYS 695 is missing expected H atoms. Skipping. Residue VAL 696 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 704 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue VAL 715 is missing expected H atoms. Skipping. Residue THR 717 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 789 is missing expected H atoms. Skipping. Residue LYS 791 is missing expected H atoms. Skipping. Residue LEU 793 is missing expected H atoms. Skipping. Residue LEU 806 is missing expected H atoms. Skipping. Residue THR 808 is missing expected H atoms. Skipping. Residue LEU 809 is missing expected H atoms. Skipping. Residue SER 825 is missing expected H atoms. Skipping. Residue LYS 829 is missing expected H atoms. Skipping. Residue LYS 851 is missing expected H atoms. Skipping. Residue SER 898 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 920 is missing expected H atoms. Skipping. Residue LYS 921 is missing expected H atoms. Skipping. Residue SER 924 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LYS 931 is missing expected H atoms. Skipping. Residue THR 947 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue THR 64 is missing expected H atoms. Skipping. Residue MET 67 is missing expected H atoms. Skipping. Residue LEU 69 is missing expected H atoms. Skipping. Residue ILE 72 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Residue SER 129 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 196 is missing expected H atoms. Skipping. Residue SER 198 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue ILE 244 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 299 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue MET 328 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue LYS 369 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LEU 379 is missing expected H atoms. Skipping. Residue LEU 396 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue LYS 401 is missing expected H atoms. Skipping. Residue ILE 408 is missing expected H atoms. Skipping. Residue LYS 452 is missing expected H atoms. Skipping. Residue ILE 461 is missing expected H atoms. Skipping. Residue LEU 462 is missing expected H atoms. Skipping. Residue LEU 477 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue LEU 490 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue LEU 502 is missing expected H atoms. Skipping. Residue VAL 530 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue THR 541 is missing expected H atoms. Skipping. Residue LEU 550 is missing expected H atoms. Skipping. Residue LYS 556 is missing expected H atoms. Skipping. Residue THR 562 is missing expected H atoms. Skipping. Residue VAL 567 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue THR 611 is missing expected H atoms. Skipping. Residue SER 634 is missing expected H atoms. Skipping. Residue THR 641 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue TYR 656 is missing expected H atoms. Skipping. Residue LEU 660 is missing expected H atoms. Skipping. Residue SER 662 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue VAL 672 is missing expected H atoms. Skipping. Residue LEU 678 is missing expected H atoms. Skipping. Residue VAL 688 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue LEU 692 is missing expected H atoms. Skipping. Residue ILE 693 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LEU 714 is missing expected H atoms. Skipping. Residue THR 717 is missing expected H atoms. Skipping. Residue MET 721 is missing expected H atoms. Skipping. Residue TYR 723 is missing expected H atoms. Skipping. Residue THR 729 is missing expected H atoms. Skipping. Residue SER 749 is missing expected H atoms. Skipping. Residue SER 754 is missing expected H atoms. Skipping. Residue SER 755 is missing expected H atoms. Skipping. Residue SER 756 is missing expected H atoms. Skipping. Residue LEU 758 is missing expected H atoms. Skipping. Residue SER 761 is missing expected H atoms. Skipping. Residue LYS 771 is missing expected H atoms. Skipping. Residue LYS 772 is missing expected H atoms. Skipping. Residue LYS 773 is missing expected H atoms. Skipping. Residue ILE 774 is missing expected H atoms. Skipping. Residue SER 776 is missing expected H atoms. Skipping. Residue VAL 778 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue LEU 793 is missing expected H atoms. Skipping. Residue THR 808 is missing expected H atoms. Skipping. Residue SER 825 is missing expected H atoms. Skipping. Residue ILE 828 is missing expected H atoms. Skipping. Residue LYS 829 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue LYS 843 is missing expected H atoms. Skipping. Residue VAL 847 is missing expected H atoms. Skipping. Residue LEU 848 is missing expected H atoms. Skipping. Residue LYS 851 is missing expected H atoms. Skipping. Residue TYR 854 is missing expected H atoms. Skipping. Residue ILE 859 is missing expected H atoms. Skipping. Residue THR 872 is missing expected H atoms. Skipping. Residue ILE 876 is missing expected H atoms. Skipping. Residue LYS 881 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LEU 892 is missing expected H atoms. Skipping. Residue LEU 893 is missing expected H atoms. Skipping. Residue LEU 896 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue LYS 921 is missing expected H atoms. Skipping. Residue SER 924 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LYS 931 is missing expected H atoms. Skipping. Residue SER 310 is missing expected H atoms. Skipping. Residue SER 325 is missing expected H atoms. Skipping. Residue SER 328 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue SER 336 is missing expected H atoms. Skipping. Residue SER 373 is missing expected H atoms. Skipping. Residue LEU 375 is missing expected H atoms. Skipping. Residue LEU 410 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue VAL 417 is missing expected H atoms. Skipping. Residue ILE 427 is missing expected H atoms. Skipping. Residue VAL 468 is missing expected H atoms. Skipping. Residue ILE 470 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue MET 541 is missing expected H atoms. Skipping. Residue SER 549 is missing expected H atoms. Skipping. Residue VAL 560 is missing expected H atoms. Skipping. Residue LEU 565 is missing expected H atoms. Skipping. Residue LYS 566 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue VAL 586 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LEU 600 is missing expected H atoms. Skipping. Residue VAL 603 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue LEU 631 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 633 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue SER 641 is missing expected H atoms. Skipping. Residue VAL 646 is missing expected H atoms. Skipping. Residue VAL 659 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 716 is missing expected H atoms. Skipping. Residue LEU 720 is missing expected H atoms. Skipping. Residue LEU 736 is missing expected H atoms. Skipping. Residue MET 738 is missing expected H atoms. Skipping. Residue VAL 742 is missing expected H atoms. Skipping. Residue LEU 745 is missing expected H atoms. Skipping. Residue MET 752 is missing expected H atoms. Skipping. Residue LEU 762 is missing expected H atoms. Skipping. Residue ALA 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue LEU 375 is missing expected H atoms. Skipping. Residue LEU 410 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue VAL 417 is missing expected H atoms. Skipping. Residue VAL 423 is missing expected H atoms. Skipping. Residue ALA 433 is missing expected H atoms. Skipping. Residue LEU 437 is missing expected H atoms. Skipping. Residue SER 467 is missing expected H atoms. Skipping. Residue VAL 468 is missing expected H atoms. Skipping. Residue ILE 470 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue ILE 481 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue LEU 495 is missing expected H atoms. Skipping. Residue LEU 496 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue VAL 560 is missing expected H atoms. Skipping. Residue LEU 565 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue VAL 569 is missing expected H atoms. Skipping. Residue LEU 571 is missing expected H atoms. Skipping. Residue SER 576 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue SER 595 is missing expected H atoms. Skipping. Residue THR 598 is missing expected H atoms. Skipping. Residue LEU 600 is missing expected H atoms. Skipping. Residue LEU 604 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue SER 641 is missing expected H atoms. Skipping. Residue LEU 663 is missing expected H atoms. Skipping. Residue LYS 665 is missing expected H atoms. Skipping. Residue VAL 668 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 694 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 700 is missing expected H atoms. Skipping. Residue LEU 730 is missing expected H atoms. Skipping. Residue SER 731 is missing expected H atoms. Skipping. Residue LYS 733 is missing expected H atoms. Skipping. Residue MET 738 is missing expected H atoms. Skipping. Residue VAL 755 is missing expected H atoms. Skipping. Residue SER 756 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ALA 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Evaluate side-chains 207 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 188 time to evaluate : 2.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 377 GLU cc_start: 0.7578 (tm-30) cc_final: 0.7189 (tm-30) REVERT: D 379 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.8370 (mt0) REVERT: C 548 PHE cc_start: 0.7886 (m-80) cc_final: 0.7597 (m-80) REVERT: C 749 ASP cc_start: 0.8647 (m-30) cc_final: 0.8367 (m-30) REVERT: C 767 ASP cc_start: 0.7480 (t70) cc_final: 0.7225 (t70) outliers start: 19 outliers final: 11 residues processed: 200 average time/residue: 0.5293 time to fit residues: 169.6957 Evaluate side-chains 191 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 179 time to evaluate : 2.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 925 PHE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain D residue 379 GLN Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 605 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 169 optimal weight: 0.8980 chunk 179 optimal weight: 0.6980 chunk 61 optimal weight: 7.9990 chunk 144 optimal weight: 0.6980 chunk 139 optimal weight: 7.9990 chunk 229 optimal weight: 3.9990 chunk 224 optimal weight: 0.9990 chunk 158 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 168 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.101429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.079821 restraints weight = 152549.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.082825 restraints weight = 69685.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.084637 restraints weight = 43478.948| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 17553 Z= 0.118 Angle : 0.703 41.219 23909 Z= 0.294 Chirality : 0.036 0.461 2964 Planarity : 0.004 0.069 3029 Dihedral : 4.438 36.202 2479 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.84 % Favored : 94.08 % Rotamer: Outliers : 1.28 % Allowed : 12.84 % Favored : 85.88 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.18), residues: 2363 helix: 1.36 (0.13), residues: 1731 sheet: -4.13 (0.75), residues: 8 loop : -1.90 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 598 HIS 0.004 0.001 HIS C 746 PHE 0.018 0.001 PHE D 383 TYR 0.014 0.001 TYR A 397 ARG 0.002 0.000 ARG C 718 Details of bonding type rmsd hydrogen bonds : bond 0.04058 ( 1252) hydrogen bonds : angle 4.62771 ( 3687) metal coordination : bond 0.01124 ( 8) metal coordination : angle 20.44542 ( 12) SS BOND : bond 0.01167 ( 5) SS BOND : angle 3.46684 ( 10) covalent geometry : bond 0.00252 (17540) covalent geometry : angle 0.52895 (23887) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 11 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue MET 76 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue ILE 103 is missing expected H atoms. Skipping. Residue SER 115 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Residue SER 129 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue SER 246 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue TYR 361 is missing expected H atoms. Skipping. Residue SER 464 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue MET 489 is missing expected H atoms. Skipping. Residue VAL 496 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue THR 504 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue THR 562 is missing expected H atoms. Skipping. Residue VAL 567 is missing expected H atoms. Skipping. Residue TYR 570 is missing expected H atoms. Skipping. Residue SER 581 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue LEU 587 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue MET 593 is missing expected H atoms. Skipping. Residue LEU 594 is missing expected H atoms. Skipping. Residue SER 595 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue ILE 599 is missing expected H atoms. Skipping. Residue THR 611 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue SER 629 is missing expected H atoms. Skipping. Residue SER 634 is missing expected H atoms. Skipping. Residue TYR 656 is missing expected H atoms. Skipping. Residue LEU 660 is missing expected H atoms. Skipping. Residue SER 662 is missing expected H atoms. Skipping. Residue ILE 677 is missing expected H atoms. Skipping. Residue LEU 679 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue LEU 692 is missing expected H atoms. Skipping. Residue ILE 693 is missing expected H atoms. Skipping. Residue LYS 695 is missing expected H atoms. Skipping. Residue VAL 696 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 704 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue VAL 715 is missing expected H atoms. Skipping. Residue THR 717 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 789 is missing expected H atoms. Skipping. Residue LYS 791 is missing expected H atoms. Skipping. Residue LEU 793 is missing expected H atoms. Skipping. Residue LEU 806 is missing expected H atoms. Skipping. Residue THR 808 is missing expected H atoms. Skipping. Residue LEU 809 is missing expected H atoms. Skipping. Residue SER 825 is missing expected H atoms. Skipping. Residue LYS 829 is missing expected H atoms. Skipping. Residue LYS 851 is missing expected H atoms. Skipping. Residue SER 898 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 920 is missing expected H atoms. Skipping. Residue LYS 921 is missing expected H atoms. Skipping. Residue SER 924 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LYS 931 is missing expected H atoms. Skipping. Residue THR 947 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue THR 64 is missing expected H atoms. Skipping. Residue MET 67 is missing expected H atoms. Skipping. Residue LEU 69 is missing expected H atoms. Skipping. Residue ILE 72 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Residue SER 129 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 196 is missing expected H atoms. Skipping. Residue SER 198 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue ILE 244 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 299 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue MET 328 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue LYS 369 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LEU 379 is missing expected H atoms. Skipping. Residue LEU 396 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue LYS 401 is missing expected H atoms. Skipping. Residue ILE 408 is missing expected H atoms. Skipping. Residue LYS 452 is missing expected H atoms. Skipping. Residue ILE 461 is missing expected H atoms. Skipping. Residue LEU 462 is missing expected H atoms. Skipping. Residue LEU 477 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue LEU 490 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue LEU 502 is missing expected H atoms. Skipping. Residue VAL 530 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue THR 541 is missing expected H atoms. Skipping. Residue LEU 550 is missing expected H atoms. Skipping. Residue LYS 556 is missing expected H atoms. Skipping. Residue THR 562 is missing expected H atoms. Skipping. Residue VAL 567 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue THR 611 is missing expected H atoms. Skipping. Residue SER 634 is missing expected H atoms. Skipping. Residue THR 641 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue TYR 656 is missing expected H atoms. Skipping. Residue LEU 660 is missing expected H atoms. Skipping. Residue SER 662 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue VAL 672 is missing expected H atoms. Skipping. Residue LEU 678 is missing expected H atoms. Skipping. Residue VAL 688 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue LEU 692 is missing expected H atoms. Skipping. Residue ILE 693 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LEU 714 is missing expected H atoms. Skipping. Residue THR 717 is missing expected H atoms. Skipping. Residue MET 721 is missing expected H atoms. Skipping. Residue TYR 723 is missing expected H atoms. Skipping. Residue THR 729 is missing expected H atoms. Skipping. Residue SER 749 is missing expected H atoms. Skipping. Residue SER 754 is missing expected H atoms. Skipping. Residue SER 755 is missing expected H atoms. Skipping. Residue SER 756 is missing expected H atoms. Skipping. Residue LEU 758 is missing expected H atoms. Skipping. Residue SER 761 is missing expected H atoms. Skipping. Residue LYS 771 is missing expected H atoms. Skipping. Residue LYS 772 is missing expected H atoms. Skipping. Residue LYS 773 is missing expected H atoms. Skipping. Residue ILE 774 is missing expected H atoms. Skipping. Residue SER 776 is missing expected H atoms. Skipping. Residue VAL 778 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue LEU 793 is missing expected H atoms. Skipping. Residue THR 808 is missing expected H atoms. Skipping. Residue SER 825 is missing expected H atoms. Skipping. Residue ILE 828 is missing expected H atoms. Skipping. Residue LYS 829 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue LYS 843 is missing expected H atoms. Skipping. Residue VAL 847 is missing expected H atoms. Skipping. Residue LEU 848 is missing expected H atoms. Skipping. Residue LYS 851 is missing expected H atoms. Skipping. Residue TYR 854 is missing expected H atoms. Skipping. Residue ILE 859 is missing expected H atoms. Skipping. Residue THR 872 is missing expected H atoms. Skipping. Residue ILE 876 is missing expected H atoms. Skipping. Residue LYS 881 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LEU 892 is missing expected H atoms. Skipping. Residue LEU 893 is missing expected H atoms. Skipping. Residue LEU 896 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue LYS 921 is missing expected H atoms. Skipping. Residue SER 924 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LYS 931 is missing expected H atoms. Skipping. Residue SER 310 is missing expected H atoms. Skipping. Residue SER 325 is missing expected H atoms. Skipping. Residue SER 328 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue SER 336 is missing expected H atoms. Skipping. Residue SER 373 is missing expected H atoms. Skipping. Residue LEU 375 is missing expected H atoms. Skipping. Residue LEU 410 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue VAL 417 is missing expected H atoms. Skipping. Residue ILE 427 is missing expected H atoms. Skipping. Residue VAL 468 is missing expected H atoms. Skipping. Residue ILE 470 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue MET 541 is missing expected H atoms. Skipping. Residue SER 549 is missing expected H atoms. Skipping. Residue VAL 560 is missing expected H atoms. Skipping. Residue LEU 565 is missing expected H atoms. Skipping. Residue LYS 566 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue VAL 586 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LEU 600 is missing expected H atoms. Skipping. Residue VAL 603 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue LEU 631 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 633 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue SER 641 is missing expected H atoms. Skipping. Residue VAL 646 is missing expected H atoms. Skipping. Residue VAL 659 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 716 is missing expected H atoms. Skipping. Residue LEU 720 is missing expected H atoms. Skipping. Residue LEU 736 is missing expected H atoms. Skipping. Residue MET 738 is missing expected H atoms. Skipping. Residue VAL 742 is missing expected H atoms. Skipping. Residue LEU 745 is missing expected H atoms. Skipping. Residue MET 752 is missing expected H atoms. Skipping. Residue LEU 762 is missing expected H atoms. Skipping. Residue ALA 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue LEU 375 is missing expected H atoms. Skipping. Residue LEU 410 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue VAL 417 is missing expected H atoms. Skipping. Residue VAL 423 is missing expected H atoms. Skipping. Residue ALA 433 is missing expected H atoms. Skipping. Residue LEU 437 is missing expected H atoms. Skipping. Residue SER 467 is missing expected H atoms. Skipping. Residue VAL 468 is missing expected H atoms. Skipping. Residue ILE 470 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue ILE 481 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue LEU 495 is missing expected H atoms. Skipping. Residue LEU 496 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue VAL 560 is missing expected H atoms. Skipping. Residue LEU 565 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue VAL 569 is missing expected H atoms. Skipping. Residue LEU 571 is missing expected H atoms. Skipping. Residue SER 576 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue SER 595 is missing expected H atoms. Skipping. Residue THR 598 is missing expected H atoms. Skipping. Residue LEU 600 is missing expected H atoms. Skipping. Residue LEU 604 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue SER 641 is missing expected H atoms. Skipping. Residue LEU 663 is missing expected H atoms. Skipping. Residue LYS 665 is missing expected H atoms. Skipping. Residue VAL 668 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 694 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 700 is missing expected H atoms. Skipping. Residue LEU 730 is missing expected H atoms. Skipping. Residue SER 731 is missing expected H atoms. Skipping. Residue LYS 733 is missing expected H atoms. Skipping. Residue MET 738 is missing expected H atoms. Skipping. Residue VAL 755 is missing expected H atoms. Skipping. Residue SER 756 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ALA 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Evaluate side-chains 226 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 205 time to evaluate : 2.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 76 MET cc_start: 0.8377 (tmm) cc_final: 0.8028 (tmm) REVERT: D 327 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8261 (mp) REVERT: D 377 GLU cc_start: 0.7582 (tm-30) cc_final: 0.7178 (tm-30) REVERT: D 379 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.8312 (mt0) REVERT: D 589 VAL cc_start: 0.8819 (OUTLIER) cc_final: 0.8565 (t) REVERT: C 548 PHE cc_start: 0.7800 (m-80) cc_final: 0.7510 (m-80) REVERT: C 749 ASP cc_start: 0.8655 (m-30) cc_final: 0.8373 (m-30) REVERT: C 767 ASP cc_start: 0.7377 (t70) cc_final: 0.7118 (t70) outliers start: 21 outliers final: 12 residues processed: 216 average time/residue: 0.5634 time to fit residues: 195.1263 Evaluate side-chains 197 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 182 time to evaluate : 2.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 925 PHE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 908 TYR Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 379 GLN Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 573 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 150 optimal weight: 8.9990 chunk 229 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 235 optimal weight: 3.9990 chunk 126 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 217 optimal weight: 1.9990 chunk 42 optimal weight: 0.0270 overall best weight: 1.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 387 ASN C 314 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.100407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.078645 restraints weight = 152891.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.081580 restraints weight = 70449.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.083361 restraints weight = 44426.799| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 17553 Z= 0.150 Angle : 0.709 40.267 23909 Z= 0.305 Chirality : 0.036 0.459 2964 Planarity : 0.004 0.068 3029 Dihedral : 4.363 36.426 2479 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.88 % Favored : 94.03 % Rotamer: Outliers : 1.16 % Allowed : 14.06 % Favored : 84.78 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.18), residues: 2363 helix: 1.48 (0.13), residues: 1729 sheet: -4.13 (0.79), residues: 8 loop : -1.90 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 598 HIS 0.010 0.001 HIS D 740 PHE 0.021 0.001 PHE B 925 TYR 0.012 0.001 TYR A 397 ARG 0.003 0.000 ARG C 703 Details of bonding type rmsd hydrogen bonds : bond 0.04055 ( 1252) hydrogen bonds : angle 4.66198 ( 3687) metal coordination : bond 0.01077 ( 8) metal coordination : angle 20.27750 ( 12) SS BOND : bond 0.01520 ( 5) SS BOND : angle 4.06020 ( 10) covalent geometry : bond 0.00317 (17540) covalent geometry : angle 0.53875 (23887) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 11 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue MET 76 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue ILE 103 is missing expected H atoms. Skipping. Residue SER 115 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Residue SER 129 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue SER 246 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue TYR 361 is missing expected H atoms. Skipping. Residue SER 464 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue MET 489 is missing expected H atoms. Skipping. Residue VAL 496 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue THR 504 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue THR 562 is missing expected H atoms. Skipping. Residue VAL 567 is missing expected H atoms. Skipping. Residue TYR 570 is missing expected H atoms. Skipping. Residue SER 581 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue LEU 587 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue MET 593 is missing expected H atoms. Skipping. Residue LEU 594 is missing expected H atoms. Skipping. Residue SER 595 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue ILE 599 is missing expected H atoms. Skipping. Residue THR 611 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue SER 629 is missing expected H atoms. Skipping. Residue SER 634 is missing expected H atoms. Skipping. Residue TYR 656 is missing expected H atoms. Skipping. Residue LEU 660 is missing expected H atoms. Skipping. Residue SER 662 is missing expected H atoms. Skipping. Residue ILE 677 is missing expected H atoms. Skipping. Residue LEU 679 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue LEU 692 is missing expected H atoms. Skipping. Residue ILE 693 is missing expected H atoms. Skipping. Residue LYS 695 is missing expected H atoms. Skipping. Residue VAL 696 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 704 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue VAL 715 is missing expected H atoms. Skipping. Residue THR 717 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 789 is missing expected H atoms. Skipping. Residue LYS 791 is missing expected H atoms. Skipping. Residue LEU 793 is missing expected H atoms. Skipping. Residue LEU 806 is missing expected H atoms. Skipping. Residue THR 808 is missing expected H atoms. Skipping. Residue LEU 809 is missing expected H atoms. Skipping. Residue SER 825 is missing expected H atoms. Skipping. Residue LYS 829 is missing expected H atoms. Skipping. Residue LYS 851 is missing expected H atoms. Skipping. Residue SER 898 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 920 is missing expected H atoms. Skipping. Residue LYS 921 is missing expected H atoms. Skipping. Residue SER 924 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LYS 931 is missing expected H atoms. Skipping. Residue THR 947 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue THR 64 is missing expected H atoms. Skipping. Residue MET 67 is missing expected H atoms. Skipping. Residue LEU 69 is missing expected H atoms. Skipping. Residue ILE 72 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Residue SER 129 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 196 is missing expected H atoms. Skipping. Residue SER 198 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue ILE 244 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 299 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue MET 328 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue LYS 369 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LEU 379 is missing expected H atoms. Skipping. Residue LEU 396 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue LYS 401 is missing expected H atoms. Skipping. Residue ILE 408 is missing expected H atoms. Skipping. Residue LYS 452 is missing expected H atoms. Skipping. Residue ILE 461 is missing expected H atoms. Skipping. Residue LEU 462 is missing expected H atoms. Skipping. Residue LEU 477 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue LEU 490 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue LEU 502 is missing expected H atoms. Skipping. Residue VAL 530 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue THR 541 is missing expected H atoms. Skipping. Residue LEU 550 is missing expected H atoms. Skipping. Residue LYS 556 is missing expected H atoms. Skipping. Residue THR 562 is missing expected H atoms. Skipping. Residue VAL 567 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue THR 611 is missing expected H atoms. Skipping. Residue SER 634 is missing expected H atoms. Skipping. Residue THR 641 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue TYR 656 is missing expected H atoms. Skipping. Residue LEU 660 is missing expected H atoms. Skipping. Residue SER 662 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue VAL 672 is missing expected H atoms. Skipping. Residue LEU 678 is missing expected H atoms. Skipping. Residue VAL 688 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue LEU 692 is missing expected H atoms. Skipping. Residue ILE 693 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LEU 714 is missing expected H atoms. Skipping. Residue THR 717 is missing expected H atoms. Skipping. Residue MET 721 is missing expected H atoms. Skipping. Residue TYR 723 is missing expected H atoms. Skipping. Residue THR 729 is missing expected H atoms. Skipping. Residue SER 749 is missing expected H atoms. Skipping. Residue SER 754 is missing expected H atoms. Skipping. Residue SER 755 is missing expected H atoms. Skipping. Residue SER 756 is missing expected H atoms. Skipping. Residue LEU 758 is missing expected H atoms. Skipping. Residue SER 761 is missing expected H atoms. Skipping. Residue LYS 771 is missing expected H atoms. Skipping. Residue LYS 772 is missing expected H atoms. Skipping. Residue LYS 773 is missing expected H atoms. Skipping. Residue ILE 774 is missing expected H atoms. Skipping. Residue SER 776 is missing expected H atoms. Skipping. Residue VAL 778 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue LEU 793 is missing expected H atoms. Skipping. Residue THR 808 is missing expected H atoms. Skipping. Residue SER 825 is missing expected H atoms. Skipping. Residue ILE 828 is missing expected H atoms. Skipping. Residue LYS 829 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue LYS 843 is missing expected H atoms. Skipping. Residue VAL 847 is missing expected H atoms. Skipping. Residue LEU 848 is missing expected H atoms. Skipping. Residue LYS 851 is missing expected H atoms. Skipping. Residue TYR 854 is missing expected H atoms. Skipping. Residue ILE 859 is missing expected H atoms. Skipping. Residue THR 872 is missing expected H atoms. Skipping. Residue ILE 876 is missing expected H atoms. Skipping. Residue LYS 881 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LEU 892 is missing expected H atoms. Skipping. Residue LEU 893 is missing expected H atoms. Skipping. Residue LEU 896 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue LYS 921 is missing expected H atoms. Skipping. Residue SER 924 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LYS 931 is missing expected H atoms. Skipping. Residue SER 310 is missing expected H atoms. Skipping. Residue SER 325 is missing expected H atoms. Skipping. Residue SER 328 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue SER 336 is missing expected H atoms. Skipping. Residue SER 373 is missing expected H atoms. Skipping. Residue LEU 375 is missing expected H atoms. Skipping. Residue LEU 410 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue VAL 417 is missing expected H atoms. Skipping. Residue ILE 427 is missing expected H atoms. Skipping. Residue VAL 468 is missing expected H atoms. Skipping. Residue ILE 470 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue MET 541 is missing expected H atoms. Skipping. Residue SER 549 is missing expected H atoms. Skipping. Residue VAL 560 is missing expected H atoms. Skipping. Residue LEU 565 is missing expected H atoms. Skipping. Residue LYS 566 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue VAL 586 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LEU 600 is missing expected H atoms. Skipping. Residue VAL 603 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue LEU 631 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 633 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue SER 641 is missing expected H atoms. Skipping. Residue VAL 646 is missing expected H atoms. Skipping. Residue VAL 659 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 716 is missing expected H atoms. Skipping. Residue LEU 720 is missing expected H atoms. Skipping. Residue LEU 736 is missing expected H atoms. Skipping. Residue MET 738 is missing expected H atoms. Skipping. Residue VAL 742 is missing expected H atoms. Skipping. Residue LEU 745 is missing expected H atoms. Skipping. Residue MET 752 is missing expected H atoms. Skipping. Residue LEU 762 is missing expected H atoms. Skipping. Residue ALA 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue LEU 375 is missing expected H atoms. Skipping. Residue LEU 410 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue VAL 417 is missing expected H atoms. Skipping. Residue VAL 423 is missing expected H atoms. Skipping. Residue ALA 433 is missing expected H atoms. Skipping. Residue LEU 437 is missing expected H atoms. Skipping. Residue SER 467 is missing expected H atoms. Skipping. Residue VAL 468 is missing expected H atoms. Skipping. Residue ILE 470 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue ILE 481 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue LEU 495 is missing expected H atoms. Skipping. Residue LEU 496 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue VAL 560 is missing expected H atoms. Skipping. Residue LEU 565 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue VAL 569 is missing expected H atoms. Skipping. Residue LEU 571 is missing expected H atoms. Skipping. Residue SER 576 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue SER 595 is missing expected H atoms. Skipping. Residue THR 598 is missing expected H atoms. Skipping. Residue LEU 600 is missing expected H atoms. Skipping. Residue LEU 604 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue SER 641 is missing expected H atoms. Skipping. Residue LEU 663 is missing expected H atoms. Skipping. Residue LYS 665 is missing expected H atoms. Skipping. Residue VAL 668 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 694 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 700 is missing expected H atoms. Skipping. Residue LEU 730 is missing expected H atoms. Skipping. Residue SER 731 is missing expected H atoms. Skipping. Residue LYS 733 is missing expected H atoms. Skipping. Residue MET 738 is missing expected H atoms. Skipping. Residue VAL 755 is missing expected H atoms. Skipping. Residue SER 756 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ALA 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Evaluate side-chains 205 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 186 time to evaluate : 2.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 377 GLU cc_start: 0.7673 (tm-30) cc_final: 0.7244 (tm-30) REVERT: D 379 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8355 (mt0) REVERT: D 589 VAL cc_start: 0.8866 (OUTLIER) cc_final: 0.8615 (t) REVERT: C 548 PHE cc_start: 0.7952 (m-80) cc_final: 0.7659 (m-80) REVERT: C 749 ASP cc_start: 0.8685 (m-30) cc_final: 0.8401 (m-30) REVERT: C 767 ASP cc_start: 0.7408 (t70) cc_final: 0.7154 (t70) outliers start: 19 outliers final: 13 residues processed: 199 average time/residue: 0.5548 time to fit residues: 175.4325 Evaluate side-chains 198 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 183 time to evaluate : 2.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 925 PHE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 676 PHE Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain D residue 379 GLN Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain C residue 411 CYS Chi-restraints excluded: chain C residue 605 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 192 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 228 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 210 optimal weight: 2.9990 chunk 205 optimal weight: 3.9990 chunk 175 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 68 optimal weight: 10.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.100316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.078524 restraints weight = 153492.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.081465 restraints weight = 70711.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.083262 restraints weight = 44386.580| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 17553 Z= 0.143 Angle : 0.709 40.065 23909 Z= 0.302 Chirality : 0.036 0.460 2964 Planarity : 0.004 0.070 3029 Dihedral : 4.306 36.222 2479 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.80 % Favored : 94.12 % Rotamer: Outliers : 1.34 % Allowed : 14.12 % Favored : 84.54 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.18), residues: 2363 helix: 1.59 (0.13), residues: 1730 sheet: -4.05 (0.86), residues: 8 loop : -1.83 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 598 HIS 0.004 0.001 HIS B 279 PHE 0.020 0.001 PHE B 707 TYR 0.013 0.001 TYR A 397 ARG 0.002 0.000 ARG C 703 Details of bonding type rmsd hydrogen bonds : bond 0.03962 ( 1252) hydrogen bonds : angle 4.59241 ( 3687) metal coordination : bond 0.00959 ( 8) metal coordination : angle 20.07303 ( 12) SS BOND : bond 0.01230 ( 5) SS BOND : angle 3.59468 ( 10) covalent geometry : bond 0.00300 (17540) covalent geometry : angle 0.54292 (23887) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 11 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue MET 76 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue ILE 103 is missing expected H atoms. Skipping. Residue SER 115 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Residue SER 129 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue SER 246 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue TYR 361 is missing expected H atoms. Skipping. Residue SER 464 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue MET 489 is missing expected H atoms. Skipping. Residue VAL 496 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue THR 504 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue THR 562 is missing expected H atoms. Skipping. Residue VAL 567 is missing expected H atoms. Skipping. Residue TYR 570 is missing expected H atoms. Skipping. Residue SER 581 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue LEU 587 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue MET 593 is missing expected H atoms. Skipping. Residue LEU 594 is missing expected H atoms. Skipping. Residue SER 595 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue ILE 599 is missing expected H atoms. Skipping. Residue THR 611 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue SER 629 is missing expected H atoms. Skipping. Residue SER 634 is missing expected H atoms. Skipping. Residue TYR 656 is missing expected H atoms. Skipping. Residue LEU 660 is missing expected H atoms. Skipping. Residue SER 662 is missing expected H atoms. Skipping. Residue ILE 677 is missing expected H atoms. Skipping. Residue LEU 679 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue LEU 692 is missing expected H atoms. Skipping. Residue ILE 693 is missing expected H atoms. Skipping. Residue LYS 695 is missing expected H atoms. Skipping. Residue VAL 696 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 704 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue VAL 715 is missing expected H atoms. Skipping. Residue THR 717 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 789 is missing expected H atoms. Skipping. Residue LYS 791 is missing expected H atoms. Skipping. Residue LEU 793 is missing expected H atoms. Skipping. Residue LEU 806 is missing expected H atoms. Skipping. Residue THR 808 is missing expected H atoms. Skipping. Residue LEU 809 is missing expected H atoms. Skipping. Residue SER 825 is missing expected H atoms. Skipping. Residue LYS 829 is missing expected H atoms. Skipping. Residue LYS 851 is missing expected H atoms. Skipping. Residue SER 898 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 920 is missing expected H atoms. Skipping. Residue LYS 921 is missing expected H atoms. Skipping. Residue SER 924 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LYS 931 is missing expected H atoms. Skipping. Residue THR 947 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue THR 64 is missing expected H atoms. Skipping. Residue MET 67 is missing expected H atoms. Skipping. Residue LEU 69 is missing expected H atoms. Skipping. Residue ILE 72 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Residue SER 129 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 196 is missing expected H atoms. Skipping. Residue SER 198 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue ILE 244 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 299 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue MET 328 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue LYS 369 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LEU 379 is missing expected H atoms. Skipping. Residue LEU 396 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue LYS 401 is missing expected H atoms. Skipping. Residue ILE 408 is missing expected H atoms. Skipping. Residue LYS 452 is missing expected H atoms. Skipping. Residue ILE 461 is missing expected H atoms. Skipping. Residue LEU 462 is missing expected H atoms. Skipping. Residue LEU 477 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue LEU 490 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue LEU 502 is missing expected H atoms. Skipping. Residue VAL 530 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue THR 541 is missing expected H atoms. Skipping. Residue LEU 550 is missing expected H atoms. Skipping. Residue LYS 556 is missing expected H atoms. Skipping. Residue THR 562 is missing expected H atoms. Skipping. Residue VAL 567 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue THR 611 is missing expected H atoms. Skipping. Residue SER 634 is missing expected H atoms. Skipping. Residue THR 641 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue TYR 656 is missing expected H atoms. Skipping. Residue LEU 660 is missing expected H atoms. Skipping. Residue SER 662 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue VAL 672 is missing expected H atoms. Skipping. Residue LEU 678 is missing expected H atoms. Skipping. Residue VAL 688 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue LEU 692 is missing expected H atoms. Skipping. Residue ILE 693 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LEU 714 is missing expected H atoms. Skipping. Residue THR 717 is missing expected H atoms. Skipping. Residue MET 721 is missing expected H atoms. Skipping. Residue TYR 723 is missing expected H atoms. Skipping. Residue THR 729 is missing expected H atoms. Skipping. Residue SER 749 is missing expected H atoms. Skipping. Residue SER 754 is missing expected H atoms. Skipping. Residue SER 755 is missing expected H atoms. Skipping. Residue SER 756 is missing expected H atoms. Skipping. Residue LEU 758 is missing expected H atoms. Skipping. Residue SER 761 is missing expected H atoms. Skipping. Residue LYS 771 is missing expected H atoms. Skipping. Residue LYS 772 is missing expected H atoms. Skipping. Residue LYS 773 is missing expected H atoms. Skipping. Residue ILE 774 is missing expected H atoms. Skipping. Residue SER 776 is missing expected H atoms. Skipping. Residue VAL 778 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue LEU 793 is missing expected H atoms. Skipping. Residue THR 808 is missing expected H atoms. Skipping. Residue SER 825 is missing expected H atoms. Skipping. Residue ILE 828 is missing expected H atoms. Skipping. Residue LYS 829 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue LYS 843 is missing expected H atoms. Skipping. Residue VAL 847 is missing expected H atoms. Skipping. Residue LEU 848 is missing expected H atoms. Skipping. Residue LYS 851 is missing expected H atoms. Skipping. Residue TYR 854 is missing expected H atoms. Skipping. Residue ILE 859 is missing expected H atoms. Skipping. Residue THR 872 is missing expected H atoms. Skipping. Residue ILE 876 is missing expected H atoms. Skipping. Residue LYS 881 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LEU 892 is missing expected H atoms. Skipping. Residue LEU 893 is missing expected H atoms. Skipping. Residue LEU 896 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue LYS 921 is missing expected H atoms. Skipping. Residue SER 924 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LYS 931 is missing expected H atoms. Skipping. Residue SER 310 is missing expected H atoms. Skipping. Residue SER 325 is missing expected H atoms. Skipping. Residue SER 328 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue SER 336 is missing expected H atoms. Skipping. Residue SER 373 is missing expected H atoms. Skipping. Residue LEU 375 is missing expected H atoms. Skipping. Residue LEU 410 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue VAL 417 is missing expected H atoms. Skipping. Residue ILE 427 is missing expected H atoms. Skipping. Residue VAL 468 is missing expected H atoms. Skipping. Residue ILE 470 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue MET 541 is missing expected H atoms. Skipping. Residue SER 549 is missing expected H atoms. Skipping. Residue VAL 560 is missing expected H atoms. Skipping. Residue LEU 565 is missing expected H atoms. Skipping. Residue LYS 566 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue VAL 586 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LEU 600 is missing expected H atoms. Skipping. Residue VAL 603 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue LEU 631 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 633 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue SER 641 is missing expected H atoms. Skipping. Residue VAL 646 is missing expected H atoms. Skipping. Residue VAL 659 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 716 is missing expected H atoms. Skipping. Residue LEU 720 is missing expected H atoms. Skipping. Residue LEU 736 is missing expected H atoms. Skipping. Residue MET 738 is missing expected H atoms. Skipping. Residue VAL 742 is missing expected H atoms. Skipping. Residue LEU 745 is missing expected H atoms. Skipping. Residue MET 752 is missing expected H atoms. Skipping. Residue LEU 762 is missing expected H atoms. Skipping. Residue ALA 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue LEU 375 is missing expected H atoms. Skipping. Residue LEU 410 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue VAL 417 is missing expected H atoms. Skipping. Residue VAL 423 is missing expected H atoms. Skipping. Residue ALA 433 is missing expected H atoms. Skipping. Residue LEU 437 is missing expected H atoms. Skipping. Residue SER 467 is missing expected H atoms. Skipping. Residue VAL 468 is missing expected H atoms. Skipping. Residue ILE 470 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue ILE 481 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue LEU 495 is missing expected H atoms. Skipping. Residue LEU 496 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue VAL 560 is missing expected H atoms. Skipping. Residue LEU 565 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue VAL 569 is missing expected H atoms. Skipping. Residue LEU 571 is missing expected H atoms. Skipping. Residue SER 576 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue SER 595 is missing expected H atoms. Skipping. Residue THR 598 is missing expected H atoms. Skipping. Residue LEU 600 is missing expected H atoms. Skipping. Residue LEU 604 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue SER 641 is missing expected H atoms. Skipping. Residue LEU 663 is missing expected H atoms. Skipping. Residue LYS 665 is missing expected H atoms. Skipping. Residue VAL 668 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 694 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 700 is missing expected H atoms. Skipping. Residue LEU 730 is missing expected H atoms. Skipping. Residue SER 731 is missing expected H atoms. Skipping. Residue LYS 733 is missing expected H atoms. Skipping. Residue MET 738 is missing expected H atoms. Skipping. Residue VAL 755 is missing expected H atoms. Skipping. Residue SER 756 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ALA 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Evaluate side-chains 212 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 190 time to evaluate : 2.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 MET cc_start: 0.7379 (mmt) cc_final: 0.6816 (mmt) REVERT: D 377 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7393 (tm-30) REVERT: D 379 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8383 (mt0) REVERT: D 589 VAL cc_start: 0.8896 (OUTLIER) cc_final: 0.8642 (t) REVERT: C 548 PHE cc_start: 0.7987 (m-80) cc_final: 0.7689 (m-80) REVERT: C 622 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.7939 (mp10) REVERT: C 749 ASP cc_start: 0.8674 (m-30) cc_final: 0.8380 (m-30) REVERT: C 767 ASP cc_start: 0.7408 (t70) cc_final: 0.7151 (t70) outliers start: 22 outliers final: 17 residues processed: 205 average time/residue: 0.5620 time to fit residues: 183.3493 Evaluate side-chains 200 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 2.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 925 PHE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 257 GLN Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 676 PHE Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain D residue 379 GLN Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain C residue 411 CYS Chi-restraints excluded: chain C residue 573 GLU Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 622 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 237 optimal weight: 4.9990 chunk 213 optimal weight: 5.9990 chunk 205 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 139 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 156 optimal weight: 6.9990 chunk 223 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 232 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.098502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.076773 restraints weight = 154981.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.079549 restraints weight = 73397.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.081218 restraints weight = 47076.169| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 17553 Z= 0.240 Angle : 0.757 41.477 23909 Z= 0.343 Chirality : 0.037 0.468 2964 Planarity : 0.005 0.070 3029 Dihedral : 4.422 36.510 2479 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.81 % Favored : 93.10 % Rotamer: Outliers : 1.22 % Allowed : 14.42 % Favored : 84.36 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.18), residues: 2363 helix: 1.34 (0.13), residues: 1736 sheet: -4.11 (0.93), residues: 8 loop : -2.00 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 652 HIS 0.005 0.001 HIS A 348 PHE 0.017 0.001 PHE A 925 TYR 0.016 0.001 TYR A 397 ARG 0.003 0.000 ARG A 912 Details of bonding type rmsd hydrogen bonds : bond 0.04274 ( 1252) hydrogen bonds : angle 4.89054 ( 3687) metal coordination : bond 0.01072 ( 8) metal coordination : angle 20.16794 ( 12) SS BOND : bond 0.01148 ( 5) SS BOND : angle 3.68710 ( 10) covalent geometry : bond 0.00496 (17540) covalent geometry : angle 0.60309 (23887) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 11 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue MET 76 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue ILE 103 is missing expected H atoms. Skipping. Residue SER 115 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Residue SER 129 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue SER 246 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue TYR 361 is missing expected H atoms. Skipping. Residue SER 464 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue MET 489 is missing expected H atoms. Skipping. Residue VAL 496 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue THR 504 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue THR 562 is missing expected H atoms. Skipping. Residue VAL 567 is missing expected H atoms. Skipping. Residue TYR 570 is missing expected H atoms. Skipping. Residue SER 581 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue LEU 587 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue MET 593 is missing expected H atoms. Skipping. Residue LEU 594 is missing expected H atoms. Skipping. Residue SER 595 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue ILE 599 is missing expected H atoms. Skipping. Residue THR 611 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue SER 629 is missing expected H atoms. Skipping. Residue SER 634 is missing expected H atoms. Skipping. Residue TYR 656 is missing expected H atoms. Skipping. Residue LEU 660 is missing expected H atoms. Skipping. Residue SER 662 is missing expected H atoms. Skipping. Residue ILE 677 is missing expected H atoms. Skipping. Residue LEU 679 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue LEU 692 is missing expected H atoms. Skipping. Residue ILE 693 is missing expected H atoms. Skipping. Residue LYS 695 is missing expected H atoms. Skipping. Residue VAL 696 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 704 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue VAL 715 is missing expected H atoms. Skipping. Residue THR 717 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 789 is missing expected H atoms. Skipping. Residue LYS 791 is missing expected H atoms. Skipping. Residue LEU 793 is missing expected H atoms. Skipping. Residue LEU 806 is missing expected H atoms. Skipping. Residue THR 808 is missing expected H atoms. Skipping. Residue LEU 809 is missing expected H atoms. Skipping. Residue SER 825 is missing expected H atoms. Skipping. Residue LYS 829 is missing expected H atoms. Skipping. Residue LYS 851 is missing expected H atoms. Skipping. Residue SER 898 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 920 is missing expected H atoms. Skipping. Residue LYS 921 is missing expected H atoms. Skipping. Residue SER 924 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LYS 931 is missing expected H atoms. Skipping. Residue THR 947 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue THR 64 is missing expected H atoms. Skipping. Residue MET 67 is missing expected H atoms. Skipping. Residue LEU 69 is missing expected H atoms. Skipping. Residue ILE 72 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Residue SER 129 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 196 is missing expected H atoms. Skipping. Residue SER 198 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue ILE 244 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 299 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue MET 328 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue LYS 369 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LEU 379 is missing expected H atoms. Skipping. Residue LEU 396 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue LYS 401 is missing expected H atoms. Skipping. Residue ILE 408 is missing expected H atoms. Skipping. Residue LYS 452 is missing expected H atoms. Skipping. Residue ILE 461 is missing expected H atoms. Skipping. Residue LEU 462 is missing expected H atoms. Skipping. Residue LEU 477 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue LEU 490 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue LEU 502 is missing expected H atoms. Skipping. Residue VAL 530 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue THR 541 is missing expected H atoms. Skipping. Residue LEU 550 is missing expected H atoms. Skipping. Residue LYS 556 is missing expected H atoms. Skipping. Residue THR 562 is missing expected H atoms. Skipping. Residue VAL 567 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue THR 611 is missing expected H atoms. Skipping. Residue SER 634 is missing expected H atoms. Skipping. Residue THR 641 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue TYR 656 is missing expected H atoms. Skipping. Residue LEU 660 is missing expected H atoms. Skipping. Residue SER 662 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue VAL 672 is missing expected H atoms. Skipping. Residue LEU 678 is missing expected H atoms. Skipping. Residue VAL 688 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue LEU 692 is missing expected H atoms. Skipping. Residue ILE 693 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LEU 714 is missing expected H atoms. Skipping. Residue THR 717 is missing expected H atoms. Skipping. Residue MET 721 is missing expected H atoms. Skipping. Residue TYR 723 is missing expected H atoms. Skipping. Residue THR 729 is missing expected H atoms. Skipping. Residue SER 749 is missing expected H atoms. Skipping. Residue SER 754 is missing expected H atoms. Skipping. Residue SER 755 is missing expected H atoms. Skipping. Residue SER 756 is missing expected H atoms. Skipping. Residue LEU 758 is missing expected H atoms. Skipping. Residue SER 761 is missing expected H atoms. Skipping. Residue LYS 771 is missing expected H atoms. Skipping. Residue LYS 772 is missing expected H atoms. Skipping. Residue LYS 773 is missing expected H atoms. Skipping. Residue ILE 774 is missing expected H atoms. Skipping. Residue SER 776 is missing expected H atoms. Skipping. Residue VAL 778 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue LEU 793 is missing expected H atoms. Skipping. Residue THR 808 is missing expected H atoms. Skipping. Residue SER 825 is missing expected H atoms. Skipping. Residue ILE 828 is missing expected H atoms. Skipping. Residue LYS 829 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue LYS 843 is missing expected H atoms. Skipping. Residue VAL 847 is missing expected H atoms. Skipping. Residue LEU 848 is missing expected H atoms. Skipping. Residue LYS 851 is missing expected H atoms. Skipping. Residue TYR 854 is missing expected H atoms. Skipping. Residue ILE 859 is missing expected H atoms. Skipping. Residue THR 872 is missing expected H atoms. Skipping. Residue ILE 876 is missing expected H atoms. Skipping. Residue LYS 881 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LEU 892 is missing expected H atoms. Skipping. Residue LEU 893 is missing expected H atoms. Skipping. Residue LEU 896 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue LYS 921 is missing expected H atoms. Skipping. Residue SER 924 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LYS 931 is missing expected H atoms. Skipping. Residue SER 310 is missing expected H atoms. Skipping. Residue SER 325 is missing expected H atoms. Skipping. Residue SER 328 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue SER 336 is missing expected H atoms. Skipping. Residue SER 373 is missing expected H atoms. Skipping. Residue LEU 375 is missing expected H atoms. Skipping. Residue LEU 410 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue VAL 417 is missing expected H atoms. Skipping. Residue ILE 427 is missing expected H atoms. Skipping. Residue VAL 468 is missing expected H atoms. Skipping. Residue ILE 470 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue MET 541 is missing expected H atoms. Skipping. Residue SER 549 is missing expected H atoms. Skipping. Residue VAL 560 is missing expected H atoms. Skipping. Residue LEU 565 is missing expected H atoms. Skipping. Residue LYS 566 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue VAL 586 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LEU 600 is missing expected H atoms. Skipping. Residue VAL 603 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue LEU 631 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 633 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue SER 641 is missing expected H atoms. Skipping. Residue VAL 646 is missing expected H atoms. Skipping. Residue VAL 659 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 716 is missing expected H atoms. Skipping. Residue LEU 720 is missing expected H atoms. Skipping. Residue LEU 736 is missing expected H atoms. Skipping. Residue MET 738 is missing expected H atoms. Skipping. Residue VAL 742 is missing expected H atoms. Skipping. Residue LEU 745 is missing expected H atoms. Skipping. Residue MET 752 is missing expected H atoms. Skipping. Residue LEU 762 is missing expected H atoms. Skipping. Residue ALA 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue LEU 375 is missing expected H atoms. Skipping. Residue LEU 410 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue VAL 417 is missing expected H atoms. Skipping. Residue VAL 423 is missing expected H atoms. Skipping. Residue ALA 433 is missing expected H atoms. Skipping. Residue LEU 437 is missing expected H atoms. Skipping. Residue SER 467 is missing expected H atoms. Skipping. Residue VAL 468 is missing expected H atoms. Skipping. Residue ILE 470 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue ILE 481 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue LEU 495 is missing expected H atoms. Skipping. Residue LEU 496 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue VAL 560 is missing expected H atoms. Skipping. Residue LEU 565 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue VAL 569 is missing expected H atoms. Skipping. Residue LEU 571 is missing expected H atoms. Skipping. Residue SER 576 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue SER 595 is missing expected H atoms. Skipping. Residue THR 598 is missing expected H atoms. Skipping. Residue LEU 600 is missing expected H atoms. Skipping. Residue LEU 604 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue SER 641 is missing expected H atoms. Skipping. Residue LEU 663 is missing expected H atoms. Skipping. Residue LYS 665 is missing expected H atoms. Skipping. Residue VAL 668 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 694 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 700 is missing expected H atoms. Skipping. Residue LEU 730 is missing expected H atoms. Skipping. Residue SER 731 is missing expected H atoms. Skipping. Residue LYS 733 is missing expected H atoms. Skipping. Residue MET 738 is missing expected H atoms. Skipping. Residue VAL 755 is missing expected H atoms. Skipping. Residue SER 756 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ALA 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Evaluate side-chains 195 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 175 time to evaluate : 2.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 MET cc_start: 0.7386 (mmt) cc_final: 0.6795 (mmt) REVERT: B 197 MET cc_start: 0.8315 (mmm) cc_final: 0.7976 (mmm) REVERT: D 377 GLU cc_start: 0.7808 (tm-30) cc_final: 0.7438 (tm-30) REVERT: D 379 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8350 (mt0) REVERT: C 548 PHE cc_start: 0.8099 (m-80) cc_final: 0.7818 (m-80) REVERT: C 622 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.8016 (mp10) REVERT: C 749 ASP cc_start: 0.8739 (m-30) cc_final: 0.8453 (m-30) REVERT: C 767 ASP cc_start: 0.7513 (t70) cc_final: 0.7266 (t70) outliers start: 20 outliers final: 14 residues processed: 188 average time/residue: 0.5533 time to fit residues: 166.5005 Evaluate side-chains 187 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 171 time to evaluate : 2.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 925 PHE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 676 PHE Chi-restraints excluded: chain D residue 379 GLN Chi-restraints excluded: chain C residue 411 CYS Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 622 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 23 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 193 optimal weight: 0.0770 chunk 35 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 231 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 149 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 overall best weight: 1.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 257 GLN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.100257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.078440 restraints weight = 152855.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.081365 restraints weight = 70389.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.083136 restraints weight = 44274.503| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 17553 Z= 0.125 Angle : 0.705 40.341 23909 Z= 0.298 Chirality : 0.036 0.461 2964 Planarity : 0.004 0.070 3029 Dihedral : 4.308 36.142 2479 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.80 % Favored : 94.12 % Rotamer: Outliers : 1.16 % Allowed : 14.73 % Favored : 84.11 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.18), residues: 2363 helix: 1.66 (0.13), residues: 1737 sheet: -3.96 (0.93), residues: 8 loop : -1.89 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 598 HIS 0.004 0.001 HIS D 740 PHE 0.017 0.001 PHE D 383 TYR 0.016 0.001 TYR A 397 ARG 0.007 0.000 ARG D 703 Details of bonding type rmsd hydrogen bonds : bond 0.03934 ( 1252) hydrogen bonds : angle 4.53734 ( 3687) metal coordination : bond 0.00849 ( 8) metal coordination : angle 19.95624 ( 12) SS BOND : bond 0.01095 ( 5) SS BOND : angle 3.39999 ( 10) covalent geometry : bond 0.00264 (17540) covalent geometry : angle 0.54124 (23887) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 11 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue MET 76 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue ILE 103 is missing expected H atoms. Skipping. Residue SER 115 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Residue SER 129 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue SER 246 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue TYR 361 is missing expected H atoms. Skipping. Residue SER 464 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue MET 489 is missing expected H atoms. Skipping. Residue VAL 496 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue THR 504 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue THR 562 is missing expected H atoms. Skipping. Residue VAL 567 is missing expected H atoms. Skipping. Residue TYR 570 is missing expected H atoms. Skipping. Residue SER 581 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue LEU 587 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue MET 593 is missing expected H atoms. Skipping. Residue LEU 594 is missing expected H atoms. Skipping. Residue SER 595 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue ILE 599 is missing expected H atoms. Skipping. Residue THR 611 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue SER 629 is missing expected H atoms. Skipping. Residue SER 634 is missing expected H atoms. Skipping. Residue TYR 656 is missing expected H atoms. Skipping. Residue LEU 660 is missing expected H atoms. Skipping. Residue SER 662 is missing expected H atoms. Skipping. Residue ILE 677 is missing expected H atoms. Skipping. Residue LEU 679 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue LEU 692 is missing expected H atoms. Skipping. Residue ILE 693 is missing expected H atoms. Skipping. Residue LYS 695 is missing expected H atoms. Skipping. Residue VAL 696 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 704 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue VAL 715 is missing expected H atoms. Skipping. Residue THR 717 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 789 is missing expected H atoms. Skipping. Residue LYS 791 is missing expected H atoms. Skipping. Residue LEU 793 is missing expected H atoms. Skipping. Residue LEU 806 is missing expected H atoms. Skipping. Residue THR 808 is missing expected H atoms. Skipping. Residue LEU 809 is missing expected H atoms. Skipping. Residue SER 825 is missing expected H atoms. Skipping. Residue LYS 829 is missing expected H atoms. Skipping. Residue LYS 851 is missing expected H atoms. Skipping. Residue SER 898 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 920 is missing expected H atoms. Skipping. Residue LYS 921 is missing expected H atoms. Skipping. Residue SER 924 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LYS 931 is missing expected H atoms. Skipping. Residue THR 947 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue THR 64 is missing expected H atoms. Skipping. Residue MET 67 is missing expected H atoms. Skipping. Residue LEU 69 is missing expected H atoms. Skipping. Residue ILE 72 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Residue SER 129 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 196 is missing expected H atoms. Skipping. Residue SER 198 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue ILE 244 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 299 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue MET 328 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue LYS 369 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LEU 379 is missing expected H atoms. Skipping. Residue LEU 396 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue LYS 401 is missing expected H atoms. Skipping. Residue ILE 408 is missing expected H atoms. Skipping. Residue LYS 452 is missing expected H atoms. Skipping. Residue ILE 461 is missing expected H atoms. Skipping. Residue LEU 462 is missing expected H atoms. Skipping. Residue LEU 477 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue LEU 490 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue LEU 502 is missing expected H atoms. Skipping. Residue VAL 530 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue THR 541 is missing expected H atoms. Skipping. Residue LEU 550 is missing expected H atoms. Skipping. Residue LYS 556 is missing expected H atoms. Skipping. Residue THR 562 is missing expected H atoms. Skipping. Residue VAL 567 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue THR 611 is missing expected H atoms. Skipping. Residue SER 634 is missing expected H atoms. Skipping. Residue THR 641 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue TYR 656 is missing expected H atoms. Skipping. Residue LEU 660 is missing expected H atoms. Skipping. Residue SER 662 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue VAL 672 is missing expected H atoms. Skipping. Residue LEU 678 is missing expected H atoms. Skipping. Residue VAL 688 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue LEU 692 is missing expected H atoms. Skipping. Residue ILE 693 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LEU 714 is missing expected H atoms. Skipping. Residue THR 717 is missing expected H atoms. Skipping. Residue MET 721 is missing expected H atoms. Skipping. Residue TYR 723 is missing expected H atoms. Skipping. Residue THR 729 is missing expected H atoms. Skipping. Residue SER 749 is missing expected H atoms. Skipping. Residue SER 754 is missing expected H atoms. Skipping. Residue SER 755 is missing expected H atoms. Skipping. Residue SER 756 is missing expected H atoms. Skipping. Residue LEU 758 is missing expected H atoms. Skipping. Residue SER 761 is missing expected H atoms. Skipping. Residue LYS 771 is missing expected H atoms. Skipping. Residue LYS 772 is missing expected H atoms. Skipping. Residue LYS 773 is missing expected H atoms. Skipping. Residue ILE 774 is missing expected H atoms. Skipping. Residue SER 776 is missing expected H atoms. Skipping. Residue VAL 778 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue LEU 793 is missing expected H atoms. Skipping. Residue THR 808 is missing expected H atoms. Skipping. Residue SER 825 is missing expected H atoms. Skipping. Residue ILE 828 is missing expected H atoms. Skipping. Residue LYS 829 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue LYS 843 is missing expected H atoms. Skipping. Residue VAL 847 is missing expected H atoms. Skipping. Residue LEU 848 is missing expected H atoms. Skipping. Residue LYS 851 is missing expected H atoms. Skipping. Residue TYR 854 is missing expected H atoms. Skipping. Residue ILE 859 is missing expected H atoms. Skipping. Residue THR 872 is missing expected H atoms. Skipping. Residue ILE 876 is missing expected H atoms. Skipping. Residue LYS 881 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LEU 892 is missing expected H atoms. Skipping. Residue LEU 893 is missing expected H atoms. Skipping. Residue LEU 896 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue LYS 921 is missing expected H atoms. Skipping. Residue SER 924 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LYS 931 is missing expected H atoms. Skipping. Residue SER 310 is missing expected H atoms. Skipping. Residue SER 325 is missing expected H atoms. Skipping. Residue SER 328 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue SER 336 is missing expected H atoms. Skipping. Residue SER 373 is missing expected H atoms. Skipping. Residue LEU 375 is missing expected H atoms. Skipping. Residue LEU 410 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue VAL 417 is missing expected H atoms. Skipping. Residue ILE 427 is missing expected H atoms. Skipping. Residue VAL 468 is missing expected H atoms. Skipping. Residue ILE 470 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue MET 541 is missing expected H atoms. Skipping. Residue SER 549 is missing expected H atoms. Skipping. Residue VAL 560 is missing expected H atoms. Skipping. Residue LEU 565 is missing expected H atoms. Skipping. Residue LYS 566 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue VAL 586 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LEU 600 is missing expected H atoms. Skipping. Residue VAL 603 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue LEU 631 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 633 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue SER 641 is missing expected H atoms. Skipping. Residue VAL 646 is missing expected H atoms. Skipping. Residue VAL 659 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 716 is missing expected H atoms. Skipping. Residue LEU 720 is missing expected H atoms. Skipping. Residue LEU 736 is missing expected H atoms. Skipping. Residue MET 738 is missing expected H atoms. Skipping. Residue VAL 742 is missing expected H atoms. Skipping. Residue LEU 745 is missing expected H atoms. Skipping. Residue MET 752 is missing expected H atoms. Skipping. Residue LEU 762 is missing expected H atoms. Skipping. Residue ALA 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue LEU 375 is missing expected H atoms. Skipping. Residue LEU 410 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue VAL 417 is missing expected H atoms. Skipping. Residue VAL 423 is missing expected H atoms. Skipping. Residue ALA 433 is missing expected H atoms. Skipping. Residue LEU 437 is missing expected H atoms. Skipping. Residue SER 467 is missing expected H atoms. Skipping. Residue VAL 468 is missing expected H atoms. Skipping. Residue ILE 470 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue ILE 481 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue LEU 495 is missing expected H atoms. Skipping. Residue LEU 496 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue VAL 560 is missing expected H atoms. Skipping. Residue LEU 565 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue VAL 569 is missing expected H atoms. Skipping. Residue LEU 571 is missing expected H atoms. Skipping. Residue SER 576 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue SER 595 is missing expected H atoms. Skipping. Residue THR 598 is missing expected H atoms. Skipping. Residue LEU 600 is missing expected H atoms. Skipping. Residue LEU 604 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue SER 641 is missing expected H atoms. Skipping. Residue LEU 663 is missing expected H atoms. Skipping. Residue LYS 665 is missing expected H atoms. Skipping. Residue VAL 668 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 694 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 700 is missing expected H atoms. Skipping. Residue LEU 730 is missing expected H atoms. Skipping. Residue SER 731 is missing expected H atoms. Skipping. Residue LYS 733 is missing expected H atoms. Skipping. Residue MET 738 is missing expected H atoms. Skipping. Residue VAL 755 is missing expected H atoms. Skipping. Residue SER 756 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ALA 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Evaluate side-chains 210 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 191 time to evaluate : 2.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 MET cc_start: 0.7449 (mmt) cc_final: 0.6930 (mmt) REVERT: A 813 MET cc_start: 0.7535 (mmp) cc_final: 0.7288 (mmp) REVERT: B 197 MET cc_start: 0.8273 (mmm) cc_final: 0.7906 (mmm) REVERT: D 377 GLU cc_start: 0.7790 (tm-30) cc_final: 0.7389 (tm-30) REVERT: D 379 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8397 (mt0) REVERT: D 589 VAL cc_start: 0.8996 (OUTLIER) cc_final: 0.8763 (t) REVERT: C 548 PHE cc_start: 0.8025 (m-80) cc_final: 0.7709 (m-80) REVERT: C 622 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.7966 (mp10) REVERT: C 749 ASP cc_start: 0.8707 (m-30) cc_final: 0.8404 (m-30) outliers start: 19 outliers final: 13 residues processed: 206 average time/residue: 0.5281 time to fit residues: 174.3512 Evaluate side-chains 198 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 182 time to evaluate : 2.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 925 PHE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 676 PHE Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 768 PHE Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain D residue 379 GLN Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain C residue 411 CYS Chi-restraints excluded: chain C residue 622 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 79 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 51 optimal weight: 8.9990 chunk 57 optimal weight: 7.9990 chunk 131 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.099534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.077870 restraints weight = 153949.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.080688 restraints weight = 71460.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.082407 restraints weight = 45345.602| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.117 17553 Z= 0.179 Angle : 0.731 41.848 23909 Z= 0.320 Chirality : 0.037 0.460 2964 Planarity : 0.004 0.070 3029 Dihedral : 4.357 36.137 2479 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.39 % Favored : 93.53 % Rotamer: Outliers : 1.10 % Allowed : 15.28 % Favored : 83.63 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.18), residues: 2363 helix: 1.57 (0.13), residues: 1740 sheet: -3.90 (0.99), residues: 8 loop : -1.92 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 652 HIS 0.004 0.001 HIS D 740 PHE 0.017 0.001 PHE A 925 TYR 0.015 0.001 TYR A 397 ARG 0.003 0.000 ARG D 703 Details of bonding type rmsd hydrogen bonds : bond 0.04051 ( 1252) hydrogen bonds : angle 4.69357 ( 3687) metal coordination : bond 0.00892 ( 8) metal coordination : angle 20.02883 ( 12) SS BOND : bond 0.02095 ( 5) SS BOND : angle 4.91346 ( 10) covalent geometry : bond 0.00380 (17540) covalent geometry : angle 0.56860 (23887) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8760.57 seconds wall clock time: 150 minutes 41.74 seconds (9041.74 seconds total)